count: 71
list:
- accessibility: null
  additionDate: '2026-01-15T12:21:20.493775Z'
  biotoolsCURIE: biotools:blast2galaxy
  biotoolsID: blast2galaxy
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: koenig@ipk-gatersleben.de
    fundrefid: null
    gridid: null
    name: Patrick König
    note: null
    orcidid: https://orcid.org/0000-0002-8948-6793
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: blast2galaxy is a Python package providing a CLI and API for performing
    BLAST+ and DIAMOND searches on Galaxy servers. It allows users to leverage the
    Galaxy API for sequence alignments and is available through package managers like
    Bioconda and Docker.
  documentation: []
  download: []
  editPermission:
    authors: []
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Database search
      uri: http://edamontology.org/operation_2421
    output: []
  homepage: https://blast2galaxy.readthedocs.io
  homepage_status: 0
  language:
  - Python
  - C
  lastUpdate: '2026-01-15T12:21:20.499617Z'
  license: MIT
  link: []
  maturity: null
  name: blast2galaxy
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1093/BIOADV/VBAE185
    metadata: null
    note: null
    pmcid: PMC11629687
    pmid: '39659591'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2017-01-13T13:16:01Z'
  biotoolsCURIE: biotools:quast
  biotoolsID: quast
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: quast.support@cab.spbu.ru
    fundrefid: null
    gridid: null
    name: QUAST Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: "QUAST stands for QUality ASsessment Tool.  \nIt evaluates a quality\
    \ of genome assemblies by computing various metrics and providing nice reports."
  documentation:
  - note: null
    type:
    - General
    url: http://quast.bioinf.spbau.ru/
  download: []
  editPermission:
    authors:
    - ELIXIR-CZ
    - Keiler_Collier
    type: group
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: quast -ek assembly.fa --out output_prefix
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: '# Running quast on a eukaryotic genome'
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    output: []
  homepage: http://quast.sourceforge.net/quast
  homepage_status: 0
  language:
  - Perl
  - Python
  - C
  lastUpdate: '2025-06-18T11:53:52.861712Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ablab/quast
  - note: null
    type:
    - Issue tracker
    url: https://github.com/ablab/quast/issues
  maturity: Mature
  name: QUAST
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1093/bioinformatics/btt086
    metadata:
      abstract: Limitations of genome sequencing techniques have led to dozens of
        assembly algorithms, none of which is perfect. A number of methods for comparing
        assemblers have been developed, but none is yet a recognized benchmark. Further,
        most existing methods for comparing assemblies are only applicable to new
        assemblies of finished genomes; the problem of evaluating assemblies of previously
        unsequenced species has not been adequately considered. Here, we present QUAST
        - a quality assessment tool for evaluating and comparing genome assemblies.
        This tool improves on leading assembly comparison software with new ideas
        and quality metrics. QUAST can evaluate assemblies both with a reference genome,
        as well as without a reference. QUAST produces many reports, summary tables
        and plots to help scientists in their research and in their publications.
        In this study, we used QUAST to compare several genome assemblers on three
        datasets. QUAST tables and plots for all of them are available in the Supplementary
        Material, and interactive versions of these reports are on the QUAST website.
        © 2013 The Author.
      authors:
      - name: Gurevich A.
      - name: Saveliev V.
      - name: Vyahhi N.
      - name: Tesler G.
      citationCount: 6872
      date: '2013-04-15T00:00:00Z'
      journal: Bioinformatics
      title: 'QUAST: Quality assessment tool for genome assemblies'
    note: null
    pmcid: PMC3624806
    pmid: '23422339'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version:
  - v.5.3.0
- accessibility: null
  additionDate: '2015-01-21T15:12:23Z'
  biotoolsCURIE: biotools:plast
  biotoolsID: plast
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: GenOuest
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: lavenier@irisa.fr
    fundrefid: null
    gridid: null
    name: Dominique Lavenier
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Parallel Local Alignment Search Tool for Database Comparison.
  documentation:
  - note: null
    type:
    - General
    url: https://plast.inria.fr/
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Sequence alignment
    operation:
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://www.irisa.fr/symbiose/projects/plast/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:06:23.702130Z'
  license: CECILL-2.0
  link: []
  maturity: Mature
  name: Plast
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: GenOuest
  publication:
  - doi: 10.1186/1471-2105-10-329
    metadata: null
    note: null
    pmcid: PMC2770072
    pmid: '19821978'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1.0'
- accessibility: null
  additionDate: '2016-02-15T10:01:52Z'
  biotoolsCURIE: biotools:besst
  biotoolsID: besst
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: nada.su.se
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Kristoffer Sahlin
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://github.com/ksahlin/BESST/issues
  description: This tool is a scaffolder. The input is a contig file and a set of
    BAM files from mapping paired-ends and/or mate-pair reads to the contigs, and
    the output are scaffolds, i.e., the contigs linked and oriented. It is both fast
    and accurate. Careful estimation of the gaps between contigs, many other scaffolders
    have seriously biased estimation. Novel treatment of paired-end contamination
    in mate-pair libraries, which identifies that some links in the MP data are better
    treated as PE.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/ksahlin/BESST
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Scaffolding
      uri: http://edamontology.org/operation_3216
    output: []
  homepage: https://github.com/ksahlin/BESST
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-25T15:40:56.757092Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ksahlin/BESST
  maturity: Mature
  name: BESST
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: arve@nada.su.se
  publication:
  - doi: 10.1186/1471-2105-15-281
    metadata: null
    note: null
    pmcid: PMC4262078
    pmid: '25128196'
    type:
    - Primary
    version: null
  - doi: 10.1101/025650
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.1093/bioinformatics/bts441
    metadata: null
    note: null
    pmcid: null
    pmid: '22923455'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2015-12-06T15:18:08Z'
  biotoolsCURIE: biotools:base
  biotoolsID: base
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: bils.se
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://base.thep.lu.se/wiki/MailingLists
  description: A comprehensive free web-based database solution for the massive amounts
    of data generated by microarray analysis.
  documentation:
  - note: null
    type:
    - General
    url: http://base.thep.lu.se/#Documentation
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Gene expression data
        uri: http://edamontology.org/data_2603
      format: []
    note: null
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
    - data:
        term: Gene expression data
        uri: http://edamontology.org/data_2603
      format: []
  homepage: http://base.thep.lu.se
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T15:37:48.836091Z'
  license: null
  link: []
  maturity: null
  name: BASE
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: mikael.borg@bils.se
  publication:
  - doi: 10.1186/1471-2105-10-330
    metadata: null
    note: null
    pmcid: PMC2768720
    pmid: '19822003'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2017-01-13T13:13:43Z'
  biotoolsCURIE: biotools:bfast
  biotoolsID: bfast
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Nils Homer
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://sourceforge.net/u/nilshomer/profile/
  description: Blat-like Fast Accurate Search Tool.
  documentation:
  - note: null
    type:
    - General
    url: https://sourceforge.net/p/bfast/wiki/Home/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genome indexing
      uri: http://edamontology.org/operation_3211
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    - term: Read mapping
      uri: http://edamontology.org/operation_3198
    output: []
  homepage: https://sourceforge.net/projects/bfast
  homepage_status: 0
  language:
  - C
  lastUpdate: '2024-11-25T15:33:02.265733Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: BFAST
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1186/1471-2105-10-175
    metadata: null
    note: null
    pmcid: PMC2709925
    pmid: '19508732'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-08-03T18:37:02Z'
  biotoolsCURIE: biotools:bless
  biotoolsID: bless
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: aramach4@illinois.edu
    fundrefid: null
    gridid: null
    name: Anand Ramachandran
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://compbio.bioen.illinois.edu/index.html
  description: BLoom-filter-based Error correction Solution for high-throughput Sequencing
    reads is a novel algorithm that produces accurate correction results with much
    less memory compared with previous solutions.
  documentation:
  - note: null
    type:
    - General
    url: https://sourceforge.net/p/bless-ec/wiki/Home/
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequencing error detection
      uri: http://edamontology.org/operation_3195
    output: []
  homepage: https://sourceforge.net/p/bless-ec/wiki/Home/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2024-11-25T15:09:41.466620Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/bless-v0p17-bloom-filter-based-error-correction-tool-for-ngs-reads.html
  maturity: null
  name: BLESS
  operatingSystem:
  - Linux
  otherID: []
  owner: mbs_import
  publication:
  - doi: 10.1093/bioinformatics/btu030
    metadata: null
    note: null
    pmcid: PMC6365934
    pmid: '24451628'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: DNA
    uri: http://edamontology.org/topic_0654
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-08-03T18:37:47Z'
  biotoolsCURIE: biotools:blasr
  biotoolsID: blasr
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: support@pacb.com
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.smrtcommunity.com/
  description: Software for mapping Single Molecule Sequencing (SMS) reads that are
    thousands of bases long, with divergence between the read and genome dominated
    by insertion and deletion error.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/PacificBiosciences/blasr
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Mapping
      uri: http://edamontology.org/operation_2429
    output: []
  homepage: https://github.com/PacificBiosciences/blasr
  homepage_status: 0
  language:
  - Shell
  - C++
  - Perl
  - Python
  lastUpdate: '2024-11-25T14:51:12.442774Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/blasr-basic-local-alignment-successive-refinement.html
  maturity: null
  name: Blasr
  operatingSystem:
  - Linux
  otherID: []
  owner: mbs_import
  publication:
  - doi: 10.1186/1471-2105-13-238
    metadata: null
    note: null
    pmcid: PMC3572422
    pmid: '22988817'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-12-18T00:14:39Z'
  biotoolsCURIE: biotools:clasp
  biotoolsID: clasp
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: christian@bioinf.uni-leipzig.de
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://hoffmann.bioinf.uni-leipzig.de/LIFE/Christian.html
  description: A fast and flexible fragment chainer that supports linear and sum-of-pair
    gap costs and uses highly time-efficient index structure, i.e., Johnson priority
    queues and range trees padded with Johnson priority queues. Chaining of short
    match fragments helps to quickly and accurately identify region of synteny that
    may not be found using common local alignment heuristics alone.
  documentation:
  - note: null
    type:
    - General
    url: http://www.bioinf.uni-leipzig.de/Software/clasp/clasp.html
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output: []
  homepage: http://www.bioinf.uni-leipzig.de/Software/clasp/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:49:34.300028Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/clasp-1-1-local-fragment-chainer-sum-of-pair-gap-costs.html
  maturity: null
  name: clasp
  operatingSystem:
  - Linux
  otherID: []
  owner: mbs_import
  publication:
  - doi: 10.1186/1748-7188-6-4
    metadata:
      abstract: 'Background: Fast seed-based alignment heuristics such as BLAST and
        BLAT have become indispensable tools in comparative genomics for all studies
        aiming at the evolutionary relations of proteins, genes, and non-coding RNAs.
        This is true in particular for the large mammalian genomes. The sensitivity
        and specificity of these tools, however, crucially depend on parameters such
        as seed sizes or maximum expectation values. In settings that require high
        sensitivity the amount of short local match fragments easily becomes intractable.
        Then, fragment chaining is a powerful leverage to quickly connect, score,
        and rank the fragments to improve the specificity.Results: Here we present
        a fast and flexible fragment chainer that for the first time also supports
        a sum-of-pair gap cost model. This model has proven to achieve a higher accuracy
        and sensitivity in its own field of application. Due to a highly time-efficient
        index structure our method outperforms the only existing tool for fragment
        chaining under the linear gap cost model. It can easily be applied to the
        output generated by alignment tools such as segemehl or BLAST. As an example
        we consider homology-based searches for human and mouse snoRNAs demonstrating
        that a highly sensitive BLAST search with subsequent chaining is an attractive
        option. The sum-of-pair gap costs provide a substantial advantage is this
        context.Conclusions: Chaining of short match fragments helps to quickly and
        accurately identify regions of homology that may not be found using local
        alignment heuristics alone. By providing both the linear and the sum-of-pair
        gap cost model, a wider range of application can be covered. The software
        clasp is available at http://www.bioinf.uni-leipzig.de/Software/clasp/. ©
        2011 Otto et al; licensee BioMed Central Ltd.'
      authors:
      - name: Otto C.
      - name: Hoffmann S.
      - name: Gorodkin J.
      - name: Stadler P.F.
      citationCount: 14
      date: '2011-03-18T00:00:00Z'
      journal: Algorithms for Molecular Biology
      title: Fast local fragment chaining using sum-of-pair gap costs
    note: null
    pmcid: PMC3072320
    pmid: '21418573'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Synteny
    uri: http://edamontology.org/topic_0102
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version:
  - '1.1'
- accessibility: null
  additionDate: '2018-06-23T11:32:20Z'
  biotoolsCURIE: biotools:dfast
  biotoolsID: dfast
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: yn@nig.ac.jp
    fundrefid: null
    gridid: null
    name: Yasukazu Nakamura
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Flexible prokaryotic genome annotation pipeline for faster genome publication.
  documentation:
  - note: null
    type:
    - General
    url: https://dfast.nig.ac.jp/faq
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output: []
  homepage: https://dfast.nig.ac.jp/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-25T14:43:43.420077Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: DFAST
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: d.gabrielaitis
  publication:
  - doi: 10.1093/bioinformatics/btx713
    metadata:
      abstract: We developed a prokaryotic genome annotation pipeline, DFAST, that
        also supports genome submission to public sequence databases. DFAST was originally
        started as an on-line annotation server, and to date, over 7000 jobs have
        been processed since its first launch in 2016. Here, we present a newly implemented
        background annotation engine for DFAST, which is also available as a standalone
        command-line program. The new engine can annotate a typical-sized bacterial
        genome within 10 min, with rich information such as pseudogenes, translation
        exceptions and orthologous gene assignment between given reference genomes.
        In addition, the modular framework of DFAST allows users to customize the
        annotation workflow easily and will also facilitate extensions for new functions
        and incorporation of new tools in the future. Availability and implementation
        The software is implemented in Python 3 and runs in both Python 2.7 and 3.4
        - on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast-core/under
        the GPLv3 license with external binaries bundled in the software distribution.
        An on-line version is also available at https://dfast.nig.ac.jp/. Contact
        yn@nig.ac.jp Supplementary informationSupplementary dataare available at Bioinformatics
        online.
      authors:
      - name: Tanizawa Y.
      - name: Fujisawa T.
      - name: Nakamura Y.
      citationCount: 770
      date: '2018-03-15T00:00:00Z'
      journal: Bioinformatics
      title: 'DFAST: A flexible prokaryotic genome annotation pipeline for faster
        genome publication'
    note: null
    pmcid: PMC5860143
    pmid: '29106469'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Web application
  topic:
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version: []
- accessibility: null
  additionDate: '2018-06-07T15:41:17Z'
  biotoolsCURIE: biotools:riblast
  biotoolsID: riblast
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: t.fukunaga@kurenai.waseda.jp
    fundrefid: null
    gridid: null
    name: Tsukasa Fukunag
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: mhamada@waseda.jp
    fundrefid: null
    gridid: null
    name: Michiaki Hamada
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: An ultrafast RNA–RNA interaction prediction system based on a seed-and-extension
    approach.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/fukunagatsu/RIblast
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Residue interaction prediction
      uri: http://edamontology.org/operation_0272
    output: []
  homepage: https://funpopgen.github.io/veqtl-mapper/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2024-11-25T14:39:24.751904Z'
  license: MIT
  link: []
  maturity: null
  name: RIblast
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: d.gabrielaitis
  publication:
  - doi: 10.1093/bioinformatics/btx287
    metadata:
      abstract: 'Motivation: LncRNAs play important roles in various biological processes.
        Although more than 58 000 human lncRNA genes have been discovered, most known
        lncRNAs are still poorly characterized. One approach to understanding the
        functions of lncRNAs is the detection of the interacting RNA target of each
        lncRNA. Because experimental detections of comprehensive lncRNA-RNA interactions
        are difficult, computational prediction of lncRNA-RNA interactions is an indispensable
        technique. However, the high computational costs of existing RNA-RNA interaction
        prediction tools prevent their application to large-scale lncRNA datasets.
        Results: Here, we present ''RIblast'', an ultrafast RNA-RNA interaction prediction
        method based on the seed-and-extension approach. RIblast discovers seed regions
        using suffix arrays and subsequently extends seed regions based on an RNA
        secondary structure energy model. Computational experiments indicate that
        RIblast achieves a level of prediction accuracy similar to those of existing
        programs, but at speeds over 64 times faster than existing programs. Availability
        and implementation: The source code of RIblast is freely available at https://github.com/fukunagatsu/RIblast
        . Contact: t.fukunaga@kurenai.waseda.jp or mhamada@waseda.jp. Supplementary
        information: Supplementary data are available at Bioinformatics online.'
      authors:
      - name: Fukunaga T.
      - name: Hamada M.
      citationCount: 77
      date: '2017-09-01T00:00:00Z'
      journal: Bioinformatics (Oxford, England)
      title: 'RIblast: an ultrafast RNA-RNA interaction prediction system based on
        a seed-and-extension approach'
    note: null
    pmcid: PMC5860064
    pmid: '28459942'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Nucleic acids
    uri: http://edamontology.org/topic_0077
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: RNA
    uri: http://edamontology.org/topic_0099
  validated: 1
  version: []
- accessibility: null
  additionDate: '2018-06-03T18:22:26Z'
  biotoolsCURIE: biotools:bart
  biotoolsID: bart
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: zang@virginia.edu
    fundrefid: null
    gridid: null
    name: Chongzhi Zang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Transcription factor prediction tool with query gene sets or epigenomic
    profiles.
  documentation:
  - note: null
    type:
    - General
    url: http://faculty.virginia.edu/zanglab/bart/#tutorial
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Transcriptional regulatory element prediction
      uri: http://edamontology.org/operation_0438
    output: []
  homepage: http://faculty.virginia.edu/zanglab/bart/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-25T14:37:18.880103Z'
  license: null
  link: []
  maturity: null
  name: BART
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: d.gabrielaitis
  publication:
  - doi: 10.1093/bioinformatics/bty194
    metadata:
      abstract: 'Summary: Identification of functional transcription factors that
        regulate a given gene set is an important problem in gene regulation studies.
        Conventional approaches for identifying transcription factors, such as DNA
        sequence motif analysis, are unable to predict functional binding of specific
        factors and not sensitive enough to detect factors binding at distal enhancers.
        Here, we present binding analysis for regulation of transcription (BART),
        a novel computational method and software package for predicting functional
        transcription factors that regulate a query gene set or associate with a query
        genomic profile, based on more than 6000 existing ChIP-seq datasets for over
        400 factors in human or mouse. This method demonstrates the advantage of utilizing
        publicly available data for functional genomics research.'
      authors:
      - name: Zhenjiawang Z.
      - name: Civelek M.
      - name: Miller C.L.
      - name: Sheffield N.C.
      - name: Guertin M.J.
      - name: Zang C.
      citationCount: 68
      date: '2018-08-15T00:00:00Z'
      journal: Bioinformatics
      title: 'BART: A transcription factor prediction tool with query gene sets or
        epigenomic profiles'
    note: null
    pmcid: PMC6084568
    pmid: '29608647'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Epigenomics
    uri: http://edamontology.org/topic_3173
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-13T13:14:36Z'
  biotoolsCURIE: biotools:flash
  biotoolsID: flash
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: flash.comment@gmail.com
    fundrefid: null
    gridid: null
    name: FLASh team
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Identifies paired-end reads which overlap in the middle, converting
    them to single long reads
  documentation: []
  download: []
  editPermission:
    authors:
    - ELIXIR-EE
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Read pre-processing
      uri: http://edamontology.org/operation_3219
    - term: Sequence merging
      uri: http://edamontology.org/operation_0232
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    output: []
  homepage: http://ccb.jhu.edu/software/FLASH/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2024-11-25T14:26:32.217431Z'
  license: null
  link: []
  maturity: null
  name: FLASH
  operatingSystem:
  - Linux
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1093/bioinformatics/btr507
    metadata:
      abstract: 'Motivation: Next-generation sequencing technologies generate very
        large numbers of short reads. Even with very deep genome coverage, short read
        lengths cause problems in de novo assemblies. The use of paired-end libraries
        with a fragment size shorter than twice the read length provides an opportunity
        to generate much longer reads by overlapping and merging read pairs before
        assembling a genome. Results: We present FLASH, a fast computational tool
        to extend the length of short reads by overlapping paired-end reads from fragment
        libraries that are sufficiently short. We tested the correctness of the tool
        on one million simulated read pairs, and we then applied it as a pre-processor
        for genome assemblies of Illumina reads from the bacterium Staphylococcus
        aureus and human chromosome 14. FLASH correctly extended and merged reads
        >99% of the time on simulated reads with an error rate of <1%. With adequately
        set parameters, FLASH correctly merged reads over 90% of the time even when
        the reads contained up to 5% errors. When FLASH was used to extend reads prior
        to assembly, the resulting assemblies had substantially greater N50 lengths
        for both contigs and scaffolds. © The Author 2011. Published by Oxford University
        Press. All rights reserved.'
      authors:
      - name: Magoc T.
      - name: Salzberg S.L.
      citationCount: 10908
      date: '2011-11-01T00:00:00Z'
      journal: Bioinformatics
      title: 'FLASH: Fast length adjustment of short reads to improve genome assemblies'
    note: null
    pmcid: PMC3198573
    pmid: '21903629'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version: []
- accessibility: null
  additionDate: '2015-08-03T09:36:26Z'
  biotoolsCURIE: biotools:blastprodom
  biotoolsID: blastprodom
  collectionID:
  - BLAST
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: BioCatalogue
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Documentor
    url: https://www.biocatalogue.org
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://prodom.prabi.fr/prodom/current/html/home.php
  description: Recursive psi-blast against the ProDom database.
  documentation:
  - note: null
    type:
    - General
    url: http://prodom.prabi.fr/prodom/current/documentation/blastProDom.html
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format: []
  homepage: http://prodom.prabi.fr/prodom/current/documentation/blastProDom.html
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:18:24.103210Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: https://www.biocatalogue.org/services/414
  maturity: null
  name: blastprodom
  operatingSystem: []
  otherID: []
  owner: BioCatalogue
  publication:
  - doi: 10.1093/bioinformatics/btg111
    metadata:
      abstract: 'Summary: A number of multifunctional, ''moonlighting'', proteins
        have been analyzed by different current programs to test wheter they identify
        both functions. PSI-BLAST and PRODOM perform best in predicting the alternative
        function.'
      authors:
      - name: Gomez A.
      - name: Domedel N.
      - name: Cedano J.
      - name: Pinol J.
      - name: Querol E.
      citationCount: 41
      date: '2003-05-01T00:00:00Z'
      journal: Bioinformatics
      title: Do current sequence analysis algorithms disclose multifunctional (moonlighting)
        proteins?
    note: null
    pmcid: null
    pmid: '12724303'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web service
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2017-12-18T00:04:25Z'
  biotoolsCURIE: biotools:blastr
  biotoolsID: blastr
  collectionID:
  - BLAST
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.tcoffee.org/Projects/blastr/#CONTACT
  description: A new method for searching Non-Coding RNAs in databases. The strategy
    we adopted relies on the use of the mutual information embedded in di-nucleotides.
    We have shown that this approach has better sensitivity and specifity than other
    softwares with comparable computational cost.
  documentation:
  - note: null
    type:
    - General
    url: http://www.tcoffee.org/Projects/blastr/#COMMANDS
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence database search
      uri: http://edamontology.org/operation_0338
    output: []
  homepage: http://www.tcoffee.org/Projects/blastr/
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2024-11-25T14:18:22.377401Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/blastr-2-1-searching-clustering-rna.html
  maturity: null
  name: BlastR
  operatingSystem:
  - Linux
  otherID: []
  owner: mbs_import
  publication:
  - doi: 10.1093/nar/gkr335
    metadata:
      abstract: We present and validate BlastR, a method for efficiently and accurately
        searching non-coding RNAs. Our approach relies on the comparison of di-nucleotides
        using BlosumR, a new log-odd substitution matrix. In order to use BlosumR
        for comparison, we recoded RNA sequences into protein-like sequences. We then
        showed that BlosumR can be used along with the BlastP algorithm in order to
        search non-coding RNA sequences. Using Rfam as a gold standard, we benchmarked
        this approach and show BlastR to be more sensitive than BlastN. We also show
        that BlastR is both faster and more sensitive than BlastP used with a single
        nucleotide log-odd substitution matrix. BlastR, when used in combination with
        WU-BlastP, is about 5 more accurate than WU-BlastN and about 50 times slower.
        The approach shown here is equally effective when combined with the NCBI-Blast
        package. The software is an open source freeware available from www.tcoffee.org/blastr.html.
        © 2011 The Author(s).
      authors:
      - name: Bussotti G.
      - name: Raineri E.
      - name: Erb I.
      - name: Zytnicki M.
      - name: Wilm A.
      - name: Beaudoing E.
      - name: Bucher P.
      - name: Notredame C.
      citationCount: 24
      date: '2011-09-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: BlastR-fast and accurate database searches for non-coding RNAs
    note: null
    pmcid: PMC3167602
    pmid: '21624887'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: RNA
    uri: http://edamontology.org/topic_0099
  - term: Data identity and mapping
    uri: http://edamontology.org/topic_3345
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  validated: 1
  version:
  - '2.2'
- accessibility: null
  additionDate: '2017-03-24T09:34:18Z'
  biotoolsCURIE: biotools:blast2srs
  biotoolsID: blast2srs
  collectionID:
  - BLAST
  confidence_flag: null
  cost: null
  credit: []
  description: Tool to retrieve protein sequences using similarity (BLAST) and keyword
    searches.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    - data:
        term: Keyword
        uri: http://edamontology.org/data_0968
      format: []
    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format: []
  homepage: http://blast2srs.embl.de/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:07:42.788285Z'
  license: null
  link: []
  maturity: null
  name: BLAST2SRS
  operatingSystem: []
  otherID: []
  owner: ELIXIR-EE
  publication:
  - doi: 10.1093/nar/gkg535
    metadata:
      abstract: 'SRS (Sequence Retrieval System) is a widely used keyword search engine
        for querying biological databases. BLAST2 is the most widely used tool to
        query databases by sequence similarity search. These tools allow users to
        retrieve sequences by shared keyword or by shared similarity, with many public
        web servers available. However, with the increasingly large datasets available
        it is now quite common that a user is interested in some subset of homologous
        sequences but has no efficient way to restrict retrieval to that set. By allowing
        the user to control SRS from the BLAST output, BLAST2SRS (http://blast2srs.embl.de/)
        aims to meet this need. This server therefore combines the two ways to search
        sequence databases: similarity and keyword. © Oxford University Press 2001.'
      authors:
      - name: Bimpikis K.
      - name: Budd A.
      - name: Linding R.
      - name: Gibson T.J.
      citationCount: 5
      date: '2003-07-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: BLAST2SRS, a web server for flexible retrieval of related protein sequences
        in the SWISS-PROT and SPTrEMBL databases
    note: null
    pmcid: PMC168942
    pmid: '12824420'
    type: []
    version: null
  relation:
  - biotoolsID: blast
    type: uses
  toolType:
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-02-14T09:35:49Z'
  biotoolsCURIE: biotools:blasto
  biotoolsID: blasto
  collectionID:
  - BLAST
  confidence_flag: null
  cost: null
  credit:
  - email: lfl@princeton.edu
    fundrefid: null
    gridid: null
    name: Laura F. Landweber
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Modified BLAST tool for searching orthologous group data. It treats
    each orthologous group as a unit and outputs a ranked list of orthologous groups
    instead of single sequences.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    output: []
  homepage: http://oxytricha.princeton.edu/BlastO/index.html
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:07:41.272053Z'
  license: null
  link: []
  maturity: null
  name: BLASTO
  operatingSystem: []
  otherID: []
  owner: ELIXIR-EE
  publication:
  - doi: 10.1093/nar/gkm278
    metadata:
      abstract: We present BLAST on Orthologous groups (BLASTO), a modified BLAST
        tool for searching orthologous group data. It treats each orthologous group
        as a unit and outputs a ranked list of orthologous groups instead of single
        sequences. By filtering out redundancy and putative paralogs, sequence comparisons
        to orthologous groups, instead of to single sequences in the database, can
        improve both functional prediction and phylogenetic inference. BLASTO computes
        the significance score of each orthologous group based on the individual BLAST
        hits in the orthologous group, using the number of taxa in the group as an
        optional weight. This allows users to control the species diversity of the
        orthologous groups. BLASTO incorporates the best-known multispecies ortholog
        databases, including NCBI Clusters of Orthologous Group, NCBI euKaryotic Orthologous
        Group database, OrthoMCL, MultiParanoid and TIGR Eukaryotic Gene Orthologues
        database, and offers a useful platform to integrate orthology information
        into functional inference and evolutionary studies of individual sequences.
        BLASTO is accessible online at http://oxytricha.princeton.edu/BlastO. © 2007
        The Author(s).
      authors:
      - name: Zhou Y.
      - name: Landweber L.F.
      citationCount: 27
      date: '2007-07-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'BLASTO: A tool for searching orthologous groups'
    note: null
    pmcid: PMC1933156
    pmid: '17483516'
    type: []
    version: null
  relation:
  - biotoolsID: blast
    type: uses
  toolType:
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version: []
- accessibility: null
  additionDate: '2018-06-04T17:08:27Z'
  biotoolsCURIE: biotools:h-blast
  biotoolsID: h-blast
  collectionID:
  - BLAST
  confidence_flag: null
  cost: null
  credit:
  - email: yux06@syr.edu
    fundrefid: null
    gridid: null
    name: Yuesheng Xu
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Fast protein sequence alignment toolkit on heterogeneous computers
    with GPUs .
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/Yeyke/H-BLAST
  download: []
  editPermission:
    authors: []
    type: private
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format: []
  homepage: https://github.com/Yeyke/H-BLAST
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:07:38.908299Z'
  license: null
  link: []
  maturity: null
  name: H-BLAST
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: d.gabrielaitis
  publication:
  - doi: 10.1093/bioinformatics/btw769
    metadata:
      abstract: 'Motivation: The sequence alignment is a fundamental problem in bioinformatics.
        BLAST is a routinely used tool for this purpose with over 118 000 citations
        in the past two decades. As the size of bio-sequence databases grows exponentially,
        the computational speed of alignment softwares must be improved. Results:
        We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool
        for a heterogeneous computer that couples CPUs and GPUs, to accelerate BLASTX
        and BLASTP - basic tools of NCBI-BLAST. H-BLAST employs a locally decoupled
        seed-extension algorithm for better performance on GPUs, and offers a performance
        tuning mechanism for better efficiency among various CPUs and GPUs combinations.
        H-BLAST produces identical alignment results as NCBI-BLAST and its computational
        speed is much faster than that of NCBI-BLAST. Speedups achieved by H-BLAST
        over sequential NCBI-BLASTP (resp. NCBI-BLASTX) range mostly from 4 to 10
        (resp. 5 to 7.2). With 2 CPU threads and 2 GPUs, H-BLAST can be faster than
        16-threaded NCBI-BLASTX. Furthermore, H-BLAST is 1.5-4 times faster than GPU-BLAST.'
      authors:
      - name: Ye W.
      - name: Chen Y.
      - name: Zhang Y.
      - name: Xu Y.
      citationCount: 22
      date: '2017-04-15T00:00:00Z'
      journal: Bioinformatics
      title: 'H-BLAST: A fast protein sequence alignment toolkit on heterogeneous
        computers with GPUs'
    note: null
    pmcid: null
    pmid: '28087515'
    type: []
    version: null
  relation:
  - biotoolsID: blast
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2016-12-19T14:24:06Z'
  biotoolsCURIE: biotools:blast_best_score
  biotoolsID: blast_best_score
  collectionID:
  - BLAST utility
  - Institut Pasteur
  - galaxyPasteur
  confidence_flag: null
  cost: null
  credit:
  - email: galaxy@pasteur.fr
    fundrefid: null
    gridid: null
    name: Galaxy Support Team
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Returns the list best hits from a list of BLAST results.
  documentation:
  - note: null
    type:
    - General
    url: https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Fodoppelt%2Fpgp_tools%2Fblast_best_score%2F0.0.1
  download: []
  editPermission:
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    type: private
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    note: null
    operation:
    - term: Pairwise sequence alignment
      uri: http://edamontology.org/operation_0491
    output:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
  homepage: https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/pgp_tools/blast_best_score/0.0.1
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T13:46:44.993503Z'
  license: null
  link:
  - note: null
    type:
    - Galaxy service
    url: https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/pgp_tools/blast_best_score/0.0.1
  maturity: Mature
  name: blast_best_score
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: hmenager
  publication:
  - doi: 10.1016/S0022-2836(05)80360-2
    metadata:
      abstract: A new approach to rapid sequence comparison, basic local alignment
        search tool (BLAST), directly approximates alignments that optimize a measure
        of local similarity, the maximal segment pair (MSP) score. Recent mathematical
        results on the stochastic properties of MSP scores allow an analysis of the
        performance of this method as well as the statistical significance of alignments
        it generates. The basic algorithm is simple and robust; it can be implemented
        in a number of ways and applied in a variety of contexts including straight-forward
        DNA and protein sequence database searches, motif searches, gene identification
        searches, and in the analysis of multiple regions of similarity in long DNA
        sequences. In addition to its flexibility and tractability to mathematical
        analysis, BLAST is an order of magnitude faster than existing sequence comparison
        tools of comparable sensitivity. © 1990, Academic Press Limited. All rights
        reserved.
      authors:
      - name: Altschul S.F.
      - name: Gish W.
      - name: Miller W.
      - name: Myers E.W.
      - name: Lipman D.J.
      citationCount: 77792
      date: '1990-01-01T00:00:00Z'
      journal: Journal of Molecular Biology
      title: Basic local alignment search tool
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gkw343
    metadata:
      abstract: High-throughput data production technologies, particularly ‘next-generation’
        DNA sequencing, have ushered in widespread and disruptive changes to biomedical
        research. Making sense of the large datasets produced by these technologies
        requires sophisticated statistical and computational methods, as well as substantial
        computational power. This has led to an acute crisis in life sciences, as
        researchers without informatics training attempt to perform computation-dependent
        analyses. Since 2005, the Galaxy project has worked to address this problem
        by providing a framework that makes advanced computational tools usable by
        non experts. Galaxy seeks to make data-intensive research more accessible,
        transparent and reproducible by providing a Web-based environment in which
        users can perform computational analyses and have all of the details automatically
        tracked for later inspection, publication, or reuse. In this report we highlight
        recently added features enabling biomedical analyses on a large scale.
      authors:
      - name: Afgan E.
      - name: Baker D.
      - name: van den Beek M.
      - name: Blankenberg D.
      - name: Bouvier D.
      - name: Cech M.
      - name: Chilton J.
      - name: Clements D.
      - name: Coraor N.
      - name: Eberhard C.
      - name: Gruning B.
      - name: Guerler A.
      - name: Hillman-Jackson J.
      - name: Kuster G.V.
      - name: Rasche E.
      - name: Soranzo N.
      - name: Turaga N.
      - name: Taylor J.
      - name: Nekrutenko A.
      - name: Goecks J.
      citationCount: 1410
      date: '2016-07-08T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The Galaxy platform for accessible, reproducible and collaborative biomedical
        analyses: 2016 update'
    note: null
    pmcid: PMC4987906
    pmid: '27137889'
    type:
    - Other
    version: null
  - doi: 10.7490/f1000research.1114334.1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Nucleic acids
    uri: http://edamontology.org/topic_0077
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  validated: 1
  version:
  - 0.0.1
- accessibility: Open access
  additionDate: '2019-08-04T10:40:53Z'
  biotoolsCURIE: biotools:BLANT
  biotoolsID: BLANT
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: whayes@uci.edu
    fundrefid: null
    gridid: null
    name: Wayne B. Hayes
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Basic Local Alignment for Networks Tool.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/waynebhayes/BLANT/blob/master/README.md
  download:
  - note: null
    type: Source code
    url: https://github.com/waynebhayes/BLANT/releases
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/waynebhayes/BLANT
  homepage_status: 0
  language:
  - C
  lastUpdate: '2024-11-24T21:06:21.947143Z'
  license: Unlicense
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/waynebhayes/BLANT/issues
  maturity: Mature
  name: BLANT
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: Ruta
  publication:
  - doi: 10.1093/bioinformatics/btz603
    metadata:
      abstract: 'BLAST creates local sequence alignments by first building a database
        of small k-letter sub-sequences called k-mers. Identical k-mers from different
        regions provide ''seeds'' for longer local alignments. This seed-and-extend
        heuristic makes BLAST extremely fast and has led to its almost exclusive use
        despite the existence of more accurate, but slower, algorithms. In this paper,
        we introduce the Basic Local Alignment for Networks Tool (BLANT). BLANT is
        the analog of BLAST, but for networks: given an input graph, it samples small,
        induced, k-node sub-graphs called k-graphlets. Graphlets have been used to
        classify networks, quantify structure, align networks both locally and globally,
        identify topology-function relationships and build taxonomic trees without
        the use of sequences. Given an input network, BLANT produces millions of graphlet
        samples in seconds - orders of magnitude faster than existing methods. BLANT
        offers sampled graphlets in various forms: distributions of graphlets or their
        orbits; graphlet degree or graphlet orbit degree vectors, the latter being
        compatible with ORCA; or an index to be used as the basis for seed-and-extend
        local alignments. We demonstrate BLANT''s usefelness by using its indexing
        mode to find functional similarity between yeast and human PPI networks.'
      authors:
      - name: Maharaj S.
      - name: Tracy B.
      - name: Hayes W.B.
      citationCount: 1
      date: '2019-12-15T00:00:00Z'
      journal: Bioinformatics
      title: BLANT - Fast graphlet sampling tool
    note: null
    pmcid: null
    pmid: '31373347'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2019-07-08T08:12:36Z'
  biotoolsCURIE: biotools:OMBlast
  biotoolsID: OMBlast
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: kevinyip@cse.cuhk.edu.hk
    fundrefid: null
    gridid: null
    name: Kevin Y. Yip
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: tf.chan@cuhk.edu.hk
    fundrefid: null
    gridid: null
    name: Ting-Fung Chan
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Alignment tool for optical mapping using a seed-and-extend approach.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/TF-Chan-Lab/OMBlast/blob/master/OMBlastManual.pdf
  - note: null
    type:
    - General
    url: https://github.com/TF-Chan-Lab/OMBlast/blob/master/README.md
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Pairwise sequence alignment
      uri: http://edamontology.org/operation_0491
    - term: Read binning
      uri: http://edamontology.org/operation_3798
    - term: Scaffolding
      uri: http://edamontology.org/operation_3216
    output: []
  homepage: https://github.com/TF-Chan-Lab/OMBlast
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2024-11-24T21:02:59.813928Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/TF-Chan-Lab/OMBlast/issues
  maturity: Mature
  name: OMBlast
  operatingSystem:
  - Linux
  - Windows
  otherID: []
  owner: Ruta
  publication:
  - doi: 10.1093/bioinformatics/btw620
    metadata:
      abstract: 'Motivation: Optical mapping is a technique for capturing fluorescent
        signal patterns of long DNA molecules (in the range of 0.1–1 Mbp). Recently,
        it has been complementing the widely used short-read sequencing technology
        by assisting with scaffolding and detecting large and complex structural variations
        (SVs). Here, we introduce a fast, robust and accurate tool called OMBlast
        for aligning optical maps, the set of signal locations on the molecules generated
        from optical mapping. Our method is based on the seed-and-extend approach
        from sequence alignment, with modifications specific to optical mapping. Results:
        Experiments with both synthetic and our real data demonstrate that OMBlast
        has higher accuracy and faster mapping speed than existing alignment methods.
        Our tool also shows significant improvement when aligning data with SVs. Availability
        and Implementation: OMBlast is implemented for Java 1.7 and is released under
        a GPL license. OMBlast can be downloaded from https://github.com/aldenleung/OMBlast
        and run directly on machines equipped with a Java virtual machine.'
      authors:
      - name: Leung A.K.-Y.
      - name: Kwok T.-P.
      - name: Wan R.
      - name: Xiao M.
      - name: Kwok P.-Y.
      - name: Yip K.Y.
      - name: Chan T.-F.
      citationCount: 25
      date: '2017-01-01T00:00:00Z'
      journal: Bioinformatics
      title: 'OMBlast: Alignment tool for optical mapping using a seed-and-extend
        approach'
    note: null
    pmcid: PMC5409310
    pmid: '28172448'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2019-10-12T11:17:16Z'
  biotoolsCURIE: biotools:Plass
  biotoolsID: Plass
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Martin Steinegger
    note: null
    orcidid: http://orcid.org/0000-0001-8781-9753
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Milot Mirdita
    note: null
    orcidid: http://orcid.org/0000-0001-8637-6719
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Johannes Söding
    note: null
    orcidid: http://orcid.org/0000-0001-9642-8244
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: 'Protein-Level ASSembler (PLASS): sensitive and precise protein assembler'
  documentation: []
  download:
  - note: null
    type: Binaries
    url: https://mmseqs.com/plass/plass-static_sse41.tar.gz
    version: Latest git static build for linux
  - note: null
    type: Binaries
    url: https://mmseqs.com/plass/plass-osx-sse41.tar.gz
    version: Latest git static build for macOS
  - note: null
    type: Container file
    url: https://hub.docker.com/r/soedinglab/plass
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: plass assemble reads_1.fastq.gz reads_2.fastq.gz assembly.fas tmp
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Assemble proteins from paired-end reads
    operation:
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    output:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://plass.mmseqs.com
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2024-11-24T20:58:12.906241Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/soedinglab/plass/issues
  - note: null
    type:
    - Repository
    url: https://github.com/soedinglab/plass
  maturity: Mature
  name: Plass
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: milot-mirdita
  publication:
  - doi: 10.1038/s41592-019-0437-4
    metadata:
      abstract: The open-source de novo protein-level assembler, Plass (https://plass.mmseqs.com),
        assembles six-frame-translated sequencing reads into protein sequences. It
        recovers 2–10 times more protein sequences from complex metagenomes and can
        assemble huge datasets. We assembled two redundancy-filtered reference protein
        catalogs, 2 billion sequences from 640 soil samples (soil reference protein
        catalog) and 292 million sequences from 775 marine eukaryotic metatranscriptomes
        (marine eukaryotic reference catalog), the largest free collections of protein
        sequences.
      authors:
      - name: Steinegger M.
      - name: Mirdita M.
      - name: Soding J.
      citationCount: 222
      date: '2019-07-01T00:00:00Z'
      journal: Nature Methods
      title: Protein-level assembly increases protein sequence recovery from metagenomic
        samples manyfold
    note: null
    pmcid: null
    pmid: '31235882'
    type:
    - Other
    version: null
  - doi: 10.1101/386110
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation:
  - biotoolsID: mmseqs2
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  validated: 1
  version:
  - 4-687d7
  - 3-764a3
  - 2-c7e35
  - 1-2e0ef
- accessibility: null
  additionDate: '2019-11-14T18:16:42Z'
  biotoolsCURIE: biotools:BJASS
  biotoolsID: BJASS
  collectionID: []
  confidence_flag: tool
  cost: null
  credit: []
  description: A new joint screening method for right-censored time-to-event data
    with ultra-high dimensional covariates | Liu, Y., Chen, X., & Li, G. (2019). A
    new joint screening method for right-censored time-to-event data with ultra-high
    dimensional covariates. Statistical methods in medical research, 0962280219864710
    | This program implements the BJASS joint screening method for DLBCL data (stored
    in matlab.mat) described in Section 4 of the paper
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Enrichment analysis
      uri: http://edamontology.org/operation_3501
    - term: Imputation
      uri: http://edamontology.org/operation_3557
    - term: Regression analysis
      uri: http://edamontology.org/operation_3659
    output: []
  homepage: https://github.com/yiucla/BJASS
  homepage_status: 0
  language:
  - MATLAB
  lastUpdate: '2024-11-24T20:56:17.282148Z'
  license: null
  link: []
  maturity: null
  name: BJASS
  operatingSystem: []
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1177/0962280219864710
    metadata:
      abstract: In an ultra-high dimensional setting with a huge number of covariates,
        variable screening is useful for dimension reduction before applying a more
        refined method for model selection and statistical analysis. This paper proposes
        a new sure joint screening procedure for right-censored time-to-event data
        based on a sparsity-restricted semiparametric accelerated failure time model.
        Our method, referred to as Buckley-James assisted sure screening (BJASS),
        consists of an initial screening step using a sparsity-restricted least-squares
        estimate based on a synthetic time variable and a refinement screening step
        using a sparsity-restricted least-squares estimate with the Buckley-James
        imputed event times. The refinement step may be repeated several times to
        obtain more stable results. We show that with any fixed number of refinement
        steps, the BJASS procedure retains all important variables with probability
        tending to 1. Simulation results are presented to illustrate its performance
        in comparison with some marginal screening methods. Real data examples are
        provided using a diffuse large-B-cell lymphoma (DLBCL) data and a breast cancer
        data. We have implemented the BJASS method using Matlab and made it available
        to readers through Github https://github.com/yiucla/BJASS.
      authors:
      - name: Liu Y.
      - name: Chen X.
      - name: Li G.
      citationCount: 7
      date: '2020-06-01T00:00:00Z'
      journal: Statistical Methods in Medical Research
      title: A new joint screening method for right-censored time-to-event data with
        ultra-high dimensional covariates
    note: null
    pmcid: PMC8285086
    pmid: '31359834'
    type: []
    version: null
  relation: []
  toolType: []
  topic: []
  validated: 1
  version: []
- accessibility: null
  additionDate: '2021-01-18T07:04:44Z'
  biotoolsCURIE: biotools:blastfrost
  biotoolsID: blastfrost
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: N.Luhmann@warwick.ac.uk
    fundrefid: null
    gridid: null
    name: Nina Luhmann
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: BlastFrost is a highly efficient method for querying 100,000s of genome
    assemblies. BlastFrost builds on the recently developed Bifrost, which generates
    a dynamic data structure for compacted and colored de Bruijn graphs from bacterial
    genomes. BlastFrost queries a Bifrost data structure for sequences of interest,
    and extracts local subgraphs, thereby enabling the efficient identification of
    the presence or absence of individual genes or single nucleotide sequence variants.
  documentation: []
  download: []
  editPermission:
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  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output: []
  homepage: https://github.com/nluhmann/BlastFrost
  homepage_status: 0
  language:
  - C++
  - Python
  lastUpdate: '2024-11-24T20:45:43.872548Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: BlastFrost
  operatingSystem: []
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  owner: Kigaard
  publication:
  - doi: 10.1101/2020.01.21.914168
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1186/s13059-020-02237-3
    metadata:
      abstract: 'BlastFrost is a highly efficient method for querying 100,000s of
        genome assemblies, building on Bifrost, a dynamic data structure for compacted
        and colored de Bruijn graphs. BlastFrost queries a Bifrost data structure
        for sequences of interest and extracts local subgraphs, enabling the identification
        of the presence or absence of individual genes or single nucleotide sequence
        variants. We show two examples using Salmonella genomes: finding within minutes
        the presence of genes in the SPI-2 pathogenicity island in a collection of
        926 genomes and identifying single nucleotide polymorphisms associated with
        fluoroquinolone resistance in three genes among 190,209 genomes. BlastFrost
        is available at https://github.com/nluhmann/BlastFrost/tree/master/data.'
      authors:
      - name: Luhmann N.
      - name: Holley G.
      - name: Achtman M.
      citationCount: 13
      date: '2021-12-01T00:00:00Z'
      journal: Genome Biology
      title: 'BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost
        graphs'
    note: null
    pmcid: PMC7798312
    pmid: '33430919'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version: []
- accessibility: null
  additionDate: '2017-01-13T13:13:51Z'
  biotoolsCURIE: biotools:blat
  biotoolsID: blat
  collectionID: []
  confidence_flag: null
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  credit:
  - email: genome@soe.ucsc.edu
    fundrefid: null
    gridid: null
    name: Website and data questions
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: genome-mirror@soe.ucsc.edu
    fundrefid: null
    gridid: null
    name: Mirror and source code questions
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: genome-www@soe.ucsc.edu
    fundrefid: null
    gridid: null
    name: Server and website access problems
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Fast, accurate spliced alignment of DNA sequences.
  documentation:
  - note: null
    type:
    - General
    url: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign
  download: []
  editPermission:
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  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output: []
  homepage: http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
  homepage_status: 0
  language:
  - C
  lastUpdate: '2024-11-24T20:35:24.102976Z'
  license: null
  link: []
  maturity: null
  name: BLAT
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  - Windows
  - Mac
  otherID:
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    version: null
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  publication:
  - doi: 10.1101/gr.229202
    metadata:
      abstract: Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species
        protein alignments. A new tool, BLAT, is more accurate and 500 times faster
        than popular existing tools for mRNA/DNA alignments and 50 times faster for
        protein alignments at sensitivity settings typically used when comparing vertebrate
        sequences. BLAT's speed stems from an index of all nonoverlapping K-mers in
        the genome. This index fits inside the RAM of inexpensive computers, and need
        only be computed once for each genome assembly. BLAT has several major stages.
        It uses the index to find regions in the genome likely to be homologous to
        the query sequence. It performs an alignment between homologous regions. It
        stitches together these aligned regions (often exons) into larger alignments
        (typically genes). Finally, BLAT revisits small internal exons possibly missed
        at the first stage and adjusts large gap boundaries that have canonical splice
        sites where feasible. This paper describes how BLAT was optimized. Effects
        on speed and sensitivity are explored for various K-mer sizes, mismatch schemes,
        and number of required index matches. BLAT is compared with other alignment
        programs on various test sets and then used in several genome-wide applications.
        http://genome.ucsc.edu hosts a web-based BLAT server for the human genome.
      authors:
      - name: Kent W.J.
      citationCount: 6684
      date: '2002-01-01T00:00:00Z'
      journal: Genome Research
      title: BLAT - The BLAST-like alignment tool
    note: null
    pmcid: PMC187518
    pmid: '11932250'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-13T13:15:13Z'
  biotoolsCURIE: biotools:last
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  credit:
  - email: last-align@googlegroups.com
    fundrefid: null
    gridid: null
    name: LAST Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Short read alignment program incorporating quality scores
  documentation:
  - note: null
    type:
    - General
    url: http://last.cbrc.jp/doc/
  download: []
  editPermission:
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  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output: []
  homepage: http://last.cbrc.jp/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2024-11-24T20:31:21.432303Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: LAST
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID:
  - type: rrid
    value: RRID:SCR_006119
    version: null
  owner: seqwiki_import
  publication:
  - doi: 10.1093/nar/gkq010
    metadata:
      abstract: New DNA sequencing technologies have achieved breakthroughs in throughput,
        at the expense of higher error rates. The primary way of interpreting biological
        sequences is via alignment, but standard alignment methods assume the sequences
        are accurate. Here, we describe how to incorporate the per-base error probabilities
        reported by sequencers into alignment. Unlike existing tools for DNA read
        mapping, our method models both sequencer errors and real sequence differences.
        This approach consistently improves mapping accuracy, even when the rate of
        real sequence difference is only 0.2%. Furthermore, when mapping Drosophila
        melanogaster reads to the Drosophila simulans genome, it increased the amount
        of correctly mapped reads from 49 to 66%. This approach enables more effective
        use of DNA reads from organisms that lack reference genomes, are extinct or
        are highly polymorphic. © The Author(s) 2010. Published by Oxford University
        Press.
      authors:
      - name: Frith M.C.
      - name: Wan R.
      - name: Horton P.
      citationCount: 63
      date: '2010-01-27T00:00:00Z'
      journal: Nucleic Acids Research
      title: Incorporating sequence quality data into alignment improves DNA read
        mapping
    note: null
    pmcid: PMC2853142
    pmid: '20110255'
    type: []
    version: null
  relation: []
  toolType:
  - Web service
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-13T13:16:56Z'
  biotoolsCURIE: biotools:vaast
  biotoolsID: vaast
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: myandell@genetics.utah.edu
    fundrefid: null
    gridid: null
    name: Mark Yandell
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Variant Annotation, Analysis and Search Tool
  documentation:
  - note: null
    type:
    - User manual
    url: http://www.yandell-lab.org/software/VAAST/VAAST_Users_Guide.pdf
  download: []
  editPermission:
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Variant prioritisation
      uri: http://edamontology.org/operation_3226
    output: []
  homepage: http://www.yandell-lab.org/software/vaast.html
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-24T20:27:12.614768Z'
  license: null
  link: []
  maturity: Mature
  name: VAAST
  operatingSystem: []
  otherID:
  - type: rrid
    value: RRID:SCR_002179
    version: null
  owner: seqwiki_import
  publication:
  - doi: 10.1016/j.ajhg.2011.05.017
    metadata:
      abstract: We have identified two families with a previously undescribed lethal
        X-linked disorder of infancy; the disorder comprises a distinct combination
        of an aged appearance, craniofacial anomalies, hypotonia, global developmental
        delays, cryptorchidism, and cardiac arrhythmias. Using X chromosome exon sequencing
        and a recently developed probabilistic algorithm aimed at discovering diseasecausing
        variants, we identified in one family a c.109T>C (p.Ser37Pro) variant in NAA10,
        a gene encoding the catalytic subunit of the major human N-terminal acetyltransferase
        (NAT). A parallel effort on a second unrelated family converged on the same
        variant. The absence of this variant in controls, the amino acid conservation
        of this region of the protein, the predicted disruptive change, and the co-occurrence
        in two unrelated families with the same rare disorder suggest that this is
        the pathogenic mutation. We confirmed this by demonstrating a significantly
        impaired biochemical activity of the mutant hNaa10p, and from this we conclude
        that a reduction in acetylation by hNaa10p causes this disease. Here we provide
        evidence of a human genetic disorder resulting from direct impairment of N-terminal
        acetylation, one of the most common protein modifications in humans. © 2011
        by The American Society of Human Genetics. All rights reserved.
      authors:
      - name: Alan F. Rope
      - name: Wang K.
      - name: Evjenth R.
      - name: Jinchuan Xing
      - name: Johnston J.J.
      - name: Swensen J.J.
      - name: Johnson W.E.
      - name: Moore B.
      - name: Huff C.D.
      - name: Bird L.M.
      - name: Carey J.C.
      - name: Opitz J.M.
      - name: Stevens C.A.
      - name: Jiang T.
      - name: Schank C.
      - name: Fain H.D.
      - name: Robison R.
      - name: Dalley B.
      - name: Chin S.
      - name: South S.T.
      - name: Theodore J. Pysher
      - name: Jorde L.B.
      - name: Hakonarson H.
      - name: Lillehaug J.R.
      - name: Biesecker L.G.
      - name: Yandell M.
      - name: Arnesen T.
      - name: Lyon G.J.
      citationCount: 190
      date: '2011-07-15T00:00:00Z'
      journal: American Journal of Human Genetics
      title: Using VAAST to identify an X-linked disorder resulting in lethality in
        male infants due to N-terminal acetyltransferase deficiency
    note: null
    pmcid: PMC3135802
    pmid: '21700266'
    type: []
    version: null
  relation: []
  toolType:
  - Suite
  topic:
  - term: DNA structural variation
    uri: http://edamontology.org/topic_3175
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2021-11-22T22:55:18.983573Z'
  biotoolsCURIE: biotools:pzlast
  biotoolsID: pzlast
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: hmori@nig.ac.jp
    fundrefid: null
    gridid: null
    name: Hiroshi Mori
    note: null
    orcidid: https://orcid.org/0000-0003-0806-7704
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ken Kurokawa
    note: null
    orcidid: https://orcid.org/0000-0001-8662-9958
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Toshikazu Ebisuzaki
    note: null
    orcidid: https://orcid.org/0000-0002-3918-1166
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ken Kurokawa
    note: null
    orcidid: https://orcid.org/0000-0001-8662-9958
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Hitoshi Ishikawa
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: An ultra-fast amino acid sequence similarity search server against
    public metagenomes.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://pzlast.riken.jp/meta/api
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    - term: Expression analysis
      uri: http://edamontology.org/operation_2495
    output: []
  homepage: https://pzlast.riken.jp/meta
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-24T20:16:05.736551Z'
  license: null
  link: []
  maturity: null
  name: PZLAST
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Jennifer
  publication:
  - doi: 10.1093/bioinformatics/btab492
    metadata:
      abstract: 'Summary:: Similarity searches of amino acid sequences against the
        public metagenomic data can provide users insights about the function of sequences
        based on the environmental distribution of similar sequences. However, a considerable
        reduction in the amount of data or the accuracy of the result was necessary
        to conduct sequence similarity searches against public metagenomic data, because
        of the vast data size more than Terabytes. Here, we present an ultra-fast
        service for the highly accurate amino acid sequence similarity search, called
        PZLAST, which can search the user''s amino acid sequences to several Terabytes
        of public metagenomic sequences in ∼10-20 min. PZLAST accomplishes its search
        speed by using PEZY-SC2, which is a Multiple Instruction Multiple Data many-core
        processor. Results of PZLAST are summarized by the ontology-based environmental
        distribution of similar sequences. PZLAST can be used to predict the function
        of sequences and mine for homologs of functionally important gene sequences.'
      authors:
      - name: Mori H.
      - name: Ishikawa H.
      - name: Higashi K.
      - name: Kato Y.
      - name: Ebisuzaki T.
      - name: Kurokawa K.
      citationCount: 4
      date: '2021-11-01T00:00:00Z'
      journal: Bioinformatics
      title: 'PZLAST: an ultra-fast amino acid sequence similarity search server against
        public metagenomes'
    note: null
    pmcid: PMC8570820
    pmid: '34240105'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Metagenomic sequencing
    uri: http://edamontology.org/topic_3837
  - term: Small molecules
    uri: http://edamontology.org/topic_0154
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-17T15:07:46Z'
  biotoolsCURIE: biotools:beast
  biotoolsID: beast
  collectionID:
  - EBI Training Tools
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://groups.google.com/group/beast-users
  description: The Bayesian Evolutionary Analysis Sampling Trees is a cross-platform
    program for Bayesian analysis of molecular sequences using MCMC (Markov chain
    Monte Carlo). It is entirely orientated towards rooted, time-measured phylogenies
    inferred using strict or relaxed molecular clock models. It can be used as a method
    of reconstructing phylogenies but is also a framework for testing evolutionary
    hypotheses without conditioning on a single tree topology.
  documentation:
  - note: null
    type:
    - General
    url: http://beast.community/first_tutorial
  download: []
  editPermission:
    authors:
    - sergitobara
    type: group
  elixirCommunity: []
  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    - term: Phylogenetic tree generation (from molecular sequences)
      uri: http://edamontology.org/operation_0540
    - term: Phylogenetic tree generation (maximum likelihood and Bayesian methods)
      uri: http://edamontology.org/operation_0547
    output: []
  homepage: http://beast.bio.ed.ac.uk/
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2024-11-24T20:07:46.590581Z'
  license: null
  link: []
  maturity: null
  name: BEAST
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ebi_training_import
  publication:
  - doi: 10.1093/molbev/mss075
    metadata:
      abstract: Computational evolutionary biology, statistical phylogenetics and
        coalescent-based population genetics are becoming increasingly central to
        the analysis and understanding of molecular sequence data. We present the
        Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package
        version 1.7, which implements a family of Markov chain Monte Carlo (MCMC)
        algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent
        analysis, phylogeography and related molecular evolutionary analyses. This
        package includes an enhanced graphical user interface program called Bayesian
        Evolutionary Analysis Utility (BEAUti) that enables access to advanced models
        for molecular sequence and phenotypic trait evolution that were previously
        available to developers only. The package also provides new tools for visualizing
        and summarizing multispecies coalescent and phylogeographic analyses. BEAUti
        and BEAST 1.7 are open source under the GNU lesser general public license
        and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk.
        © The Author 2012. Published by Oxford University Press on behalf of the Society
        for Molecular Biology and Evolution. All rights reserved.
      authors:
      - name: Drummond A.J.
      - name: Suchard M.A.
      - name: Xie D.
      - name: Rambaut A.
      citationCount: 8490
      date: '2012-08-01T00:00:00Z'
      journal: Molecular Biology and Evolution
      title: Bayesian phylogenetics with BEAUti and the BEAST 1.7
    note: null
    pmcid: PMC3408070
    pmid: '22367748'
    type: []
    version: null
  - doi: 10.1093/ve/vey016
    metadata: null
    note: null
    pmcid: PMC6007674
    pmid: '29942656'
    type: []
    version: null
  - doi: 10.1186/1471-2148-7-214
    metadata:
      abstract: 'Background. The evolutionary analysis of molecular sequence variation
        is a statistical enterprise. This is reflected in the increased use of probabilistic
        models for phylogenetic inference, multiple sequence alignment, and molecular
        population genetics. Here we present BEAST: a fast, flexible software architecture
        for Bayesian analysis of molecular sequences related by an evolutionary tree.
        A large number of popular stochastic models of sequence evolution are provided
        and tree-based models suitable for both within- and between-species sequence
        data are implemented. Results. BEAST version 1.4.6 consists of 81000 lines
        of Java source code, 779 classes and 81 packages. It provides models for DNA
        and protein sequence evolution, highly parametric coalescent analysis, relaxed
        clock phylogenetics, non-contemporaneous sequence data, statistical alignment
        and a wide range of options for prior distributions. BEAST source code is
        object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/
        under the GNU LGPL license. Conclusion. BEAST is a powerful and flexible evolutionary
        analysis package for molecular sequence variation. It also provides a resource
        for the further development of new models and statistical methods of evolutionary
        analysis. © 2007 Drummond and Rambaut; licensee BioMed Central Ltd.'
      authors:
      - name: Drummond A.J.
      - name: Rambaut A.
      citationCount: 10833
      date: '2007-12-01T00:00:00Z'
      journal: BMC Evolutionary Biology
      title: 'BEAST: Bayesian evolutionary analysis by sampling trees'
    note: null
    pmcid: PMC2247476
    pmid: '17996036'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-03-01T15:34:10Z'
  biotoolsCURIE: biotools:blast2go
  biotoolsID: blast2go
  collectionID:
  - BLAST
  confidence_flag: null
  cost: null
  credit:
  - email: contact@biobam.com
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://www.biobam.com/biobam-contact/
  description: Bioinformatics platform for high-quality functional annotation and
    analysis of genomic datasets. It allows analyzing and visualizing newly sequenced
    genomes by combining state-of-the-art methodologies, standard resources and algorithms.
    It allows to gain biological insights fast and easy even for completely novel
    genomes. Perform out-of-the-box the entire workflow of functional annotation of
    your transcriptomic datasets including its analysis and biological interpretation.
  documentation:
  - note: null
    type:
    - General
    url: https://www.blast2go.com/blast2go-pro
  download: []
  editPermission:
    authors:
    - sergitobara
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment (nucleic acid)
        uri: http://edamontology.org/data_1383
      format: []
    note: null
    operation:
    - term: Gene functional annotation
      uri: http://edamontology.org/operation_3672
    output:
    - data:
        term: Over-representation data
        uri: http://edamontology.org/data_3753
      format: []
  homepage: https://www.blast2go.com/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-24T15:59:58.360493Z'
  license: null
  link: []
  maturity: null
  name: Blast2GO
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ELIXIR-EE
  publication:
  - doi: 10.1093/bioinformatics/bti610
    metadata:
      abstract: 'Summary: We present here Blast2GO (B2G), a research tool designed
        with the main purpose of enabling Gene Ontology (GO) based data mining on
        sequence data for which no GO annotation is yet available. B2G joints in one
        application GO annotation based on similarity searches with statistical analysis
        and highlighted visualization on directed acyclic graphs. This tool offers
        a suitable platform for functional genomics research in non-model species.
        B2G is an intuitive and interactive desktop application that allows monitoring
        and comprehension of the whole annotation and analysis process. © The Author
        2005. Published by Oxford University Press. All rights reserved.'
      authors:
      - name: Conesa A.
      - name: Gotz S.
      - name: Garcia-Gomez J.M.
      - name: Terol J.
      - name: Talon M.
      - name: Robles M.
      citationCount: 9378
      date: '2005-09-15T00:00:00Z'
      journal: Bioinformatics
      title: 'Blast2GO: A universal tool for annotation, visualization and analysis
        in functional genomics research'
    note: null
    pmcid: null
    pmid: '16081474'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkn176
    metadata:
      abstract: 'Functional genomics technologies have been widely adopted in the
        biological research of both model and non-model species. An efficient functional
        annotation of DNA or protein sequences is a major requirement for the successful
        application of these approaches as functional information on gene products
        is often the key to the interpretation of experimental results. Therefore,
        there is an increasing need for bioinformatics resources which are able to
        cope with large amount of sequence data, produce valuable annotation results
        and are easily accessible to laboratories where functional genomics projects
        are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented
        solution for the high-throughput and automatic functional annotation of DNA
        or protein sequences based on the Gene Ontology vocabulary. The most outstanding
        Blast2GO features are: (i) the combination of various annotation strategies
        and tools controlling type and intensity of annotation, (ii) the numerous
        graphical features such as the interactive GO-graph visualization for gene-set
        function profiling or descriptive charts, (iii) the general sequence management
        features and (iv) high-throughput capabilities. We used the Blast2GO framework
        to carry out a detailed analysis of annotation behaviour through homology
        transfer and its impact in functional genomics research. Our aim is to offer
        biologists useful information to take into account when addressing the task
        of functionally characterizing their sequence data. © 2008 The Author(s).'
      authors:
      - name: Gotz S.
      - name: Garcia-Gomez J.M.
      - name: Terol J.
      - name: Williams T.D.
      - name: Nagaraj S.H.
      - name: Nueda M.J.
      - name: Robles M.
      - name: Talon M.
      - name: Dopazo J.
      - name: Conesa A.
      citationCount: 3322
      date: '2008-06-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: High-throughput functional annotation and data mining with the Blast2GO
        suite
    note: null
    pmcid: PMC2425479
    pmid: '18445632'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Nucleic acid sites, features and motifs
    uri: http://edamontology.org/topic_3511
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2017-01-13T13:13:50Z'
  biotoolsCURIE: biotools:blast
  biotoolsID: blast
  collectionID:
  - BLAST
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: blast-help@ncbi.nlm.nih.gov
    fundrefid: null
    gridid: null
    name: BLAST Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: A tool that finds regions of similarity between biological sequences.
    The program compares nucleotide or protein sequences to sequence databases and
    calculates the statistical significance.
  documentation:
  - note: null
    type:
    - General
    url: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs
  - note: null
    type:
    - Citation instructions
    url: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=References
  download: []
  editPermission:
    authors:
    - ELIXIR-EE
    - sergitobara
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: BLAST XML results format
        uri: http://edamontology.org/format_3331
      - term: BLAST XML v2 results format
        uri: http://edamontology.org/format_3836
      - term: TSV
        uri: http://edamontology.org/format_3475
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: ASN.1 sequence format
        uri: http://edamontology.org/format_1966
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: Binary format
        uri: http://edamontology.org/format_2333
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-24T15:55:00.707215Z'
  license: null
  link: []
  maturity: Mature
  name: BLAST
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1016/S0022-2836(05)80360-2
    metadata:
      abstract: A new approach to rapid sequence comparison, basic local alignment
        search tool (BLAST), directly approximates alignments that optimize a measure
        of local similarity, the maximal segment pair (MSP) score. Recent mathematical
        results on the stochastic properties of MSP scores allow an analysis of the
        performance of this method as well as the statistical significance of alignments
        it generates. The basic algorithm is simple and robust; it can be implemented
        in a number of ways and applied in a variety of contexts including straight-forward
        DNA and protein sequence database searches, motif searches, gene identification
        searches, and in the analysis of multiple regions of similarity in long DNA
        sequences. In addition to its flexibility and tractability to mathematical
        analysis, BLAST is an order of magnitude faster than existing sequence comparison
        tools of comparable sensitivity. © 1990, Academic Press Limited. All rights
        reserved.
      authors:
      - name: Altschul S.F.
      - name: Gish W.
      - name: Miller W.
      - name: Myers E.W.
      - name: Lipman D.J.
      citationCount: 77781
      date: '1990-01-01T00:00:00Z'
      journal: Journal of Molecular Biology
      title: Basic local alignment search tool
    note: null
    pmcid: null
    pmid: '2231712'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btw305
    metadata:
      abstract: 'Motivation: Over the last decades, vast numbers of sequences were
        deposited in public databases. Bioinformatics tools allow homology and consequently
        functional inference for these sequences. New profile-based homology search
        tools have been introduced, allowing reliable detection of remote homologs,
        but have not been systematically benchmarked. To provide such a comparison,
        which can guide bioinformatics workflows, we extend and apply our previously
        developed benchmark approach to evaluate the ''next generation'' of profile-based
        approaches, including CS-BLAST, HHSEARCH and PHMMER, in comparison with the
        non-profile based search tools NCBI-BLAST, USEARCH, UBLAST and FASTA. Method:
        We generated challenging benchmark datasets based on protein domain architectures
        within either the PFAM + Clan, SCOP/Superfamily or CATH/Gene3D domain definition
        schemes. From each dataset, homologous and non-homologous protein pairs were
        aligned using each tool, and standard performance metrics calculated. We further
        measured congruence of domain architecture assignments in the three domain
        databases. Results: CSBLAST and PHMMER had overall highest accuracy. FASTA,
        UBLAST and USEARCH showed large trade-offs of accuracy for speed optimization.
        Conclusion: Profile methods are superior at inferring remote homologs but
        the difference in accuracy between methods is relatively small. PHMMER and
        CSBLAST stand out with the highest accuracy, yet still at a reasonable computational
        cost. Additionally, we show that less than 0.1% of Swiss-Prot protein pairs
        considered homologous by one database are considered non-homologous by another,
        implying that these classifications represent equivalent underlying biological
        phenomena, differing mostly in coverage and granularity. Availability and
        Implementation: Benchmark datasets and all scripts are placed at (http://sonnhammer.org/download/Homology-benchmark).'
      authors:
      - name: Saripella G.V.
      - name: Sonnhammer E.L.L.
      - name: Forslund K.
      citationCount: 8
      date: '2016-09-01T00:00:00Z'
      journal: Bioinformatics
      title: Benchmarking the next generation of homology inference tools
    note: null
    pmcid: PMC5013910
    pmid: '27256311'
    type:
    - Benchmarking study
    version: null
  - doi: 10.1093/nar/gkn201
    metadata:
      abstract: Basic Local Alignment Search Tool (BLAST) is a sequence similarity
        search program. The public interface of BLAST, http://www.ncbi.nlm.nih.gov/blast,
        at the NCBI website has recently been reengineered to improve usability and
        performance. Key new features include simplified search forms, improved navigation,
        a list of recent BLAST results, saved search strategies and a documentation
        directory. Here, we describe the BLAST web application's new features, explain
        design decisions and outline plans for future improvement.
      authors:
      - name: Johnson M.
      - name: Zaretskaya I.
      - name: Raytselis Y.
      - name: Merezhuk Y.
      - name: McGinnis S.
      - name: Madden T.L.
      citationCount: 2950
      date: '2008-01-01T00:00:00Z'
      journal: Nucleic acids research
      title: 'NCBI BLAST: a better web interface.'
    note: null
    pmcid: PMC2447716
    pmid: '18440982'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkt282
    metadata:
      abstract: The Basic Local Alignment Search Tool (BLAST) website at the National
        Center for Biotechnology (NCBI) is an important resource for searching and
        aligning sequences. A new BLAST report allows faster loading of alignments,
        adds navigation aids, allows easy downloading of subject sequences and reports
        and has improved usability. Here, we describe these improvements to the BLAST
        report, discuss design decisions, describe other improvements to the search
        page and database documentation and outline plans for future development.
        The NCBI BLAST URL is http://blast.ncbi.nlm.nih.gov.
      authors:
      - name: Boratyn G.M.
      - name: Camacho C.
      - name: Cooper P.S.
      - name: Coulouris G.
      - name: Fong A.
      - name: Ma N.
      - name: Madden T.L.
      - name: Matten W.T.
      - name: McGinnis S.D.
      - name: Merezhuk Y.
      - name: Raytselis Y.
      - name: Sayers E.W.
      - name: Tao T.
      - name: Ye J.
      - name: Zaretskaya I.
      citationCount: 887
      date: '2013-01-01T00:00:00Z'
      journal: Nucleic acids research
      title: 'BLAST: a more efficient report with usability improvements.'
    note: null
    pmcid: PMC3692093
    pmid: '23609542'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Web application
  - Web API
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2023-10-15T19:46:30.952186Z'
  biotoolsCURIE: biotools:blaze
  biotoolsID: blaze
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: hee.shim@unimelb.edu.au
    fundrefid: null
    gridid: null
    name: Heejung Shim
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: michael.clark@unimelb.edu.au
    fundrefid: null
    gridid: null
    name: Michael B. Clark
    note: null
    orcidid: https://orcid.org/0000-0002-2903-9537
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Identification of cell barcodes from long-read single-cell RNA-seq
    with BLAZE.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Demultiplexing
      uri: http://edamontology.org/operation_3933
    - term: Quantification
      uri: http://edamontology.org/operation_3799
    - term: Base-calling
      uri: http://edamontology.org/operation_3185
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: DNA barcoding
      uri: http://edamontology.org/operation_3200
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://github.com/shimlab/BLAZE
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-11-24T14:37:46.683552Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: BLAZE
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1186/s13059-023-02907-y
    metadata:
      abstract: Long-read single-cell RNA sequencing (scRNA-seq) enables the quantification
        of RNA isoforms in individual cells. However, long-read scRNA-seq using the
        Oxford Nanopore platform has largely relied upon matched short-read data to
        identify cell barcodes. We introduce BLAZE, which accurately and efficiently
        identifies 10x cell barcodes using only nanopore long-read scRNA-seq data.
        BLAZE outperforms the existing tools and provides an accurate representation
        of the cells present in long-read scRNA-seq when compared to matched short
        reads. BLAZE simplifies long-read scRNA-seq while improving the results, is
        compatible with downstream tools accepting a cell barcode file, and is available
        at https://github.com/shimlab/BLAZE.
      authors:
      - name: You Y.
      - name: Prawer Y.D.J.
      - name: De Paoli-Iseppi R.
      - name: Hunt C.P.J.
      - name: Parish C.L.
      - name: Shim H.
      - name: Clark M.B.
      citationCount: 14
      date: '2023-12-01T00:00:00Z'
      journal: Genome Biology
      title: Identification of cell barcodes from long-read single-cell RNA-seq with
        BLAZE
    note: null
    pmcid: PMC10077662
    pmid: '37024980'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Script
  topic:
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: RNA
    uri: http://edamontology.org/topic_0099
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-01-03T21:43:37.162391Z'
  biotoolsCURIE: biotools:flust
  biotoolsID: flust
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: ingvild.k.ekroll@ntnu.no
    fundrefid: null
    gridid: null
    name: Ingvild Kinn Ekroll
    note: null
    orcidid: https://orcid.org/0000-0002-0540-0201
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: A fast, open source framework for ultrasound blood flow simulations.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Phasing
      uri: http://edamontology.org/operation_3454
    - term: Spectral analysis
      uri: http://edamontology.org/operation_3214
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    output: []
  homepage: http://www.ustb.no/flust
  homepage_status: 0
  language:
  - MATLAB
  lastUpdate: '2024-11-24T14:23:39.864727Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://bitbucket.org/ustb/ustb/src/master/
  maturity: null
  name: FLUST
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1016/j.cmpb.2023.107604
    metadata:
      abstract: 'Background and objective:Ultrasound based blood velocity estimation
        is a continuously developing frontier, where the vast number of possible acquisition
        setups and velocity estimators makes it challenging to assess which combination
        is better suited for a given imaging application. FLUST, the Flow-Line based
        Ultrasound Simulation Tool, may be used to address this challenge, providing
        a common platform for evaluation of velocity estimation schemes on in silico
        data. However, the FLUST approach had some limitations in its original form,
        including reduced robustness for phase sensitive setups and the need for manual
        selection of integrity parameters. In addition, implementation of the technique
        and therefore also documentation of signal integrity was left to potential
        users of the approach. Methods: In this work, several improvements to the
        FLUST technique are proposed and investigated, and a robust, open source simulation
        framework developed. The software supports several transducer types and acquisition
        setups, in addition to a range of different flow phantoms. The main goal of
        this work is to offer a robust, computationally cheap and user-friendly framework
        to simulate ultrasound data from stationary blood velocity fields and thereby
        facilitate design and evaluation of estimation schemes, including acquisition
        design, velocity estimation and other post-processing steps. Results: The
        technical improvements proposed in this work resulted in reduced interpolation
        errors, reduced variability in signal power, and also automatic selection
        of spatial and temporal discretization parameters. Results are presented illustrating
        the challenges and the effectiveness of the solutions. The integrity of the
        improved simulation framework is validated in an extensive study, with results
        indicating that speckle statistics, spatial and temporal correlation and frequency
        content all correspond well with theoretical predictions. Finally, an illustrative
        example shows how FLUST may be used throughout the design and optimization
        process of a velocity estimator. Conclusions: The FLUST framework is available
        as a part of the UltraSound ToolBox (USTB), and the results in this paper
        demonstrate that it can be used as an efficient and reliable tool for the
        development and validation of ultrasound-based velocity estimation schemes.'
      authors:
      - name: Ekroll I.K.
      - name: Saris A.E.C.M.
      - name: Avdal J.
      citationCount: 3
      date: '2023-08-01T00:00:00Z'
      journal: Computer Methods and Programs in Biomedicine
      title: 'FLUST: A fast, open source framework for ultrasound blood flow simulations'
    note: null
    pmcid: null
    pmid: '37220679'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Suite
  topic:
  - term: Echography
    uri: http://edamontology.org/topic_3954
  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Medical imaging
    uri: http://edamontology.org/topic_3384
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-03-06T10:49:13.850578Z'
  biotoolsCURIE: biotools:maast
  biotoolsID: maast
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: kpollard@gladstone.ucsf.edu
    fundrefid: null
    gridid: null
    name: Katherine S. Pollard
    note: null
    orcidid: https://orcid.org/0000-0002-9870-6196
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Zhou Jason Shi
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Stephen Nayfach
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Genotyping thousands of microbial strains. Type SNPs from a set of
    whole genome assemblies and sequencing reads from beginning to end in one single
    command line.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    - term: SNP detection
      uri: http://edamontology.org/operation_0484
    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    output: []
  homepage: https://github.com/zjshi/Maast
  homepage_status: 0
  language:
  - Python
  - C++
  lastUpdate: '2024-11-24T14:12:40.938372Z'
  license: MIT
  link: []
  maturity: null
  name: Maast
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1186/s13059-023-03030-8
    metadata:
      abstract: Existing single nucleotide polymorphism (SNP) genotyping algorithms
        do not scale for species with thousands of sequenced strains, nor do they
        account for conspecific redundancy. Here we present a bioinformatics tool,
        Maast, which empowers population genetic meta-analysis of microbes at an unrivaled
        scale. Maast implements a novel algorithm to heuristically identify a minimal
        set of diverse conspecific genomes, then constructs a reliable SNP panel for
        each species, and enables rapid and accurate genotyping using a hybrid of
        whole-genome alignment and k-mer exact matching. We demonstrate Maast’s utility
        by genotyping thousands of Helicobacter pylori strains and tracking SARS-CoV-2
        diversification.
      authors:
      - name: Shi Z.J.
      - name: Nayfach S.
      - name: Pollard K.S.
      citationCount: 3
      date: '2023-12-01T00:00:00Z'
      journal: Genome Biology
      title: 'Maast: genotyping thousands of microbial strains efficiently'
    note: null
    pmcid: PMC10416524
    pmid: '37563669'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Workflow
  topic:
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 0
  version: []
- accessibility: null
  additionDate: '2015-01-29T15:47:52Z'
  biotoolsCURIE: biotools:blast_ebi
  biotoolsID: blast_ebi
  collectionID:
  - BLAST
  - EBI Tools
  - Job Dispatcher Tools
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: EMBL-EBI
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: NCBI
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Job Dispatcher
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Primary contact
    url: https://www.ebi.ac.uk/jdispatcher
  description: Find regions of sequence similarity and alignments between a query
    sequence and database sequences.
  documentation:
  - note: null
    type:
    - Terms of use
    url: http://www.ebi.ac.uk/about/terms-of-use
  - note: null
    type:
    - General
    url: https://www.ebi.ac.uk/jdispatcher/help
  - note: null
    type:
    - General
    url: https://blast.ncbi.nlm.nih.gov/Blast.cgi
  download:
  - note: null
    type: Downloads page
    url: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
    version: null
  editPermission:
    authors:
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    - sergitobara
    - nandana
    type: group
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  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format: []
  homepage: https://www.ebi.ac.uk/jdispatcher/sss/ncbiblast
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-24T13:59:15.809077Z'
  license: null
  link:
  - note: null
    type:
    - Helpdesk
    url: https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services
  maturity: null
  name: BLAST (EBI)
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: jdispatcher
  publication:
  - doi: 10.1186/1471-2105-10-421
    metadata:
      abstract: 'Background: Sequence similarity searching is a very important bioinformatics
        task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods
        through its use of heuristics, the speed of the current BLAST software is
        suboptimal for very long queries or database sequences. There are also some
        shortcomings in the user-interface of the current command-line applications.Results:
        We describe features and improvements of rewritten BLAST software and introduce
        new command-line applications. Long query sequences are broken into chunks
        for processing, in some cases leading to dramatically shorter run times. For
        long database sequences, it is possible to retrieve only the relevant parts
        of the sequence, reducing CPU time and memory usage for searches of short
        queries against databases of contigs or chromosomes. The program can now retrieve
        masking information for database sequences from the BLAST databases. A new
        modular software library can now access subject sequence data from arbitrary
        data sources. We introduce several new features, including strategy files
        that allow a user to save and reuse their favorite set of options. The strategy
        files can be uploaded to and downloaded from the NCBI BLAST web site.Conclusion:
        The new BLAST command-line applications, compared to the current BLAST tools,
        demonstrate substantial speed improvements for long queries as well as chromosome
        length database sequences. We have also improved the user interface of the
        command-line applications. © 2009 Camacho et al; licensee BioMed Central Ltd.'
      authors:
      - name: Camacho C.
      - name: Coulouris G.
      - name: Avagyan V.
      - name: Ma N.
      - name: Papadopoulos J.
      - name: Bealer K.
      - name: Madden T.L.
      citationCount: 12681
      date: '2009-12-15T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'BLAST+: Architecture and applications'
    note: null
    pmcid: PMC2803857
    pmid: '20003500'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkae241
    metadata:
      abstract: The EMBL-EBI Job Dispatcher sequence analysis tools framework (https://www.ebi.ac.uk/jdispatcher)
        enables the scientific community to perform a diverse range of sequence analyses
        using popular bioinformatics applications. Free access to the tools and required
        sequence datasets is provided through user-friendly web applications, as well
        as via RESTful and SOAP-based APIs. These are integrated into popular EMBL-EBI
        resources such as UniProt, InterPro, ENA and Ensembl Genomes. This paper overviews
        recent improvements to Job Dispatcher, including its brand new website and
        documentation, enhanced visualisations, improved job management, and a rising
        trend of user reliance on the service from low- and middle-income regions.
      authors:
      - name: Madeira F.
      - name: Madhusoodanan N.
      - name: Lee J.
      - name: Eusebi A.
      - name: Niewielska A.
      - name: Tivey A.R.N.
      - name: Lopez R.
      - name: Butcher S.
      citationCount: 60
      date: '2024-07-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024
    note: null
    pmcid: PMC11223882
    pmid: '38597606'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gkac240
    metadata:
      abstract: The EMBL-EBI search and sequence analysis tools frameworks provide
        integrated access to EMBL-EBI's data resources and core bioinformatics analytical
        tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search
        engine across nearly 5 billion entries, while the Job Dispatcher tools framework
        (https://www.ebi.ac.uk/services) enables the scientific community to perform
        a diverse range of sequence analysis using popular bioinformatics applications.
        Both allow users to interact through user-friendly web applications, as well
        as via RESTful and SOAP-based APIs. Here, we describe recent improvements
        to these services and updates made to accommodate the increasing data requirements
        during the COVID-19 pandemic.
      authors:
      - name: Madeira F.
      - name: Pearce M.
      - name: Tivey A.R.N.
      - name: Basutkar P.
      - name: Lee J.
      - name: Edbali O.
      - name: Madhusoodanan N.
      - name: Kolesnikov A.
      - name: Lopez R.
      citationCount: 1248
      date: '2022-07-05T00:00:00Z'
      journal: Nucleic Acids Research
      title: Search and sequence analysis tools services from EMBL-EBI in 2022
    note: null
    pmcid: PMC9252731
    pmid: '35412617'
    type:
    - Other
    version: null
  relation:
  - biotoolsID: blast
    type: uses
  toolType:
  - Web API
  - Web application
  - Web service
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2017-03-24T11:45:04Z'
  biotoolsCURIE: biotools:etblast
  biotoolsID: etblast
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Textual similarity search engine. This server can parse and summarize
    the results of an abstract similarity search to find appropriate journals for
    publication, authors with expertise in a given field, and documents similar to
    a submitted query.
  documentation: []
  download: []
  editPermission:
    authors:
    - Rodrigo
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    - term: Structural similarity search
      uri: http://edamontology.org/operation_0360
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output: []
  homepage: http://etest.vbi.vt.edu/etblast3/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-24T13:50:59.099089Z'
  license: null
  link: []
  maturity: null
  name: eTBLAST
  operatingSystem: []
  otherID: []
  owner: ELIXIR-EE
  publication:
  - doi: 10.1093/bioinformatics/btl388
    metadata:
      abstract: 'Motivation: The most widely used literature search techniques, such
        as those offered by NCBI''s PubMed system, require significant effort on the
        part of the searcher, and inexperienced searchers do not use these systems
        as effectively as experienced users. Improved literature search engines can
        save researchers time and effort by making it easier to locate the most important
        and relevant literature. Results: We have created and optimized a new, hybrid
        search system for Medline that takes natural text as input and then delivers
        results with high precision and recall. The combination of a fast, low-sensitivity
        weighted keyword-based first pass algorithm to cast a wide net to gather an
        initial set of literature, followed by a unique sentence-alignment based similarity
        algorithm to rank order those results was developed that is sensitive, fast
        and easy to use. Several text similarity search algorithms, both standard
        and novel, were implemented and tested in order to determine which obtained
        the best results in information retrieval exercises. © 2006 Oxford University
        Press.'
      authors:
      - name: Lewis J.
      - name: Ossowski S.
      - name: Hicks J.
      - name: Errami M.
      - name: Garner H.R.
      citationCount: 80
      date: '2006-09-15T00:00:00Z'
      journal: Bioinformatics
      title: 'Text similarity: An alternative way to search MEDLINE'
    note: null
    pmcid: null
    pmid: '16926219'
    type: []
    version: null
  - doi: 10.1093/nar/gkm221
    metadata:
      abstract: Authors, editors and reviewers alike use the biomedical literature
        to identify appropriate journals in which to publish, potential reviewers
        for papers or grants, and collaborators (or competitors) with similar interests.
        Traditionally, this process has either relied upon personal expertise and
        knowledge or upon a somewhat unsystematic and laborious process of manually
        searching through the literature for trends. To help with these tasks, we
        report three utilities that parse and summarize the results of an abstract
        similarity search to find appropriate journals for publication, authors with
        expertise in a given field, and documents similar to a submitted query. The
        utilities are based upon a program, eTBLAST, designed to identify similar
        documents within literature databases such as (but not limited to) MEDLINE.
        These services are freely accessible through the Internet at http://invention.swmed.edu/etblast/
        etblast.shtml, where users can upload a file or paste text such as an abstract
        into the browser interface. © 2007 The Author(s).
      authors:
      - name: Errami M.
      - name: Wren J.D.
      - name: Hicks J.M.
      - name: Garner H.R.
      citationCount: 73
      date: '2007-07-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'ETBLAST: A web server to identify expert reviewers, appropriate journals
        and similar publications'
    note: null
    pmcid: PMC1933238
    pmid: '17452348'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Natural language processing
    uri: http://edamontology.org/topic_0218
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2024-11-04T16:09:05.874785Z'
  biotoolsCURIE: biotools:blastxml_to_top_descr
  biotoolsID: blastxml_to_top_descr
  collectionID:
  - BLAST
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: This tool is a short Python script to parse a BLAST XML file, and extract
    the identifiers with description for the top matches (by default the top 3), and
    output these as a simple tabular file along with the query identifiers.
  documentation: []
  download: []
  editPermission:
    authors:
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    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    - term: Sequence annotation
      uri: http://edamontology.org/operation_0361
    output: []
  homepage: https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-07T15:03:21.144398Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/peterjc/galaxy_blast
  - note: null
    type:
    - Issue tracker
    url: https://github.com/peterjc/galaxy_blast/issues
  maturity: Mature
  name: blastxml_to_top_descr
  operatingSystem: []
  otherID: []
  owner: rlibouban
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2024-11-04T15:57:03.137603Z'
  biotoolsCURIE: biotools:blast_rbh
  biotoolsID: blast_rbh
  collectionID:
  - BLAST
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: This tool is a short Python script to run reciprocal BLAST searches
    on a pair of sequence files, and extract the reciprocal best hits.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Gene functional annotation
      uri: http://edamontology.org/operation_3672
    - term: Nucleic acid sequence analysis
      uri: http://edamontology.org/operation_2478
    output: []
  homepage: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-07T10:09:35.127184Z'
  license: MIT
  link: []
  maturity: Mature
  name: blast_rbh
  operatingSystem: []
  otherID: []
  owner: rlibouban
  publication:
  - doi: 10.1186/s13742-015-0080-7
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1186/1471-2105-10-421
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Nucleic acid sites, features and motifs
    uri: http://edamontology.org/topic_3511
  validated: 0
  version: []
- accessibility: null
  additionDate: '2021-05-26T19:33:15Z'
  biotoolsCURIE: biotools:boost
  biotoolsID: boost
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Boost is a set of libraries for the C++ programming language that provides
    support for tasks and structures such as linear algebra, pseudorandom number generation,
    multithreading, image processing, regular expressions, and unit testing.
  documentation:
  - note: null
    type:
    - General
    url: https://www.boost.org/doc/
  - note: Guide for Windows
    type:
    - Installation instructions
    url: https://www.boost.org/doc/libs/1_76_0/more/getting_started/windows.html
  - note: Guide for Unix variants (MacOS, Linux)
    type:
    - Installation instructions
    url: https://www.boost.org/doc/libs/1_76_0/more/getting_started/unix-variants.html
  - note: null
    type:
    - General
    url: https://github.com/boostorg/wiki/wiki
  download:
  - note: null
    type: Downloads page
    url: https://www.boost.org/users/download/
    version: null
  editPermission:
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    type: private
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Regular expression
        uri: http://edamontology.org/data_1352
      format:
      - term: Workflow format
        uri: http://edamontology.org/format_2032
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format: []
    note: null
    operation:
    - term: Image analysis
      uri: http://edamontology.org/operation_3443
    output: []
  homepage: https://www.boost.org/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2022-11-30T22:14:55.756466Z'
  license: Other
  link:
  - note: null
    type:
    - Mailing list
    url: https://www.boost.org/community/groups.html
  maturity: null
  name: Boost
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication: []
  relation: []
  toolType:
  - Library
  topic:
  - term: Pure mathematics
    uri: http://edamontology.org/topic_3570
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Software engineering
    uri: http://edamontology.org/topic_3372
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2017-02-13T08:26:09Z'
  biotoolsCURIE: biotools:blast_viewer
  biotoolsID: blast_viewer
  collectionID:
  - BLAST utility
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Patrick Durand
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://github.com/pgdurand/BlastViewer/issues
  - email: null
    fundrefid: null
    gridid: null
    name: Plealog
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Provider
    url: http://www.plealog.com
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://github.com/pgdurand/BlastViewer/issues
  description: Tool that aims at displaying in a graphical way results from the NCBI
    BLAST software.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/pgdurand/BlastViewer/wiki
  download:
  - note: null
    type: Software package
    url: https://github.com/pgdurand/BlastViewer/releases
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Pairwise sequence alignment
      uri: http://edamontology.org/operation_0491
    - term: Phylogenetic tree visualisation
      uri: http://edamontology.org/operation_0567
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output: []
  homepage: https://github.com/pgdurand/BlastViewer
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2022-11-23T16:02:07.032792Z'
  license: AGPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/pgdurand/BlastViewer
  maturity: Mature
  name: BLAST Viewer
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: patrick@plealog.com
  publication: []
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 1
  version:
  - 5.5.2
- accessibility: Open access
  additionDate: '2022-04-19T21:57:51.024607Z'
  biotoolsCURIE: biotools:blastxml_to_gapped_gff3
  biotoolsID: blastxml_to_gapped_gff3
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: Convert BlastXML results into GFF3 format.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output: []
  homepage: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/blastxml_to_gapped_gff3/blastxml_to_gapped_gff3/1.1
  homepage_status: 0
  language: []
  lastUpdate: '2022-04-24T10:30:55.335883Z'
  license: Not licensed
  link: []
  maturity: null
  name: blastxml to gapped gff3
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: Jennifer
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Literature and language
    uri: http://edamontology.org/topic_3068
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2022-03-21T19:32:59.198217Z'
  biotoolsCURIE: biotools:rmblast
  biotoolsID: rmblast
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Arian Smit
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Robert Hubley
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Jeb Rosen
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: RMBlast is a RepeatMasker compatible version of the standard NCBI blastn
    program. The primary difference between this distribution and the NCBI distribution
    is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output: []
  homepage: http://www.repeatmasker.org/RMBlast.html
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2022-03-21T19:32:59.200849Z'
  license: OSL-2.1
  link: []
  maturity: null
  name: RMBlast
  operatingSystem:
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  - Linux
  otherID: []
  owner: Chan019
  publication: []
  relation:
  - biotoolsID: repeatmasker
    type: uses
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 1
  version:
  - 2.11.0
- accessibility: Open access
  additionDate: '2021-12-12T14:42:49.495448Z'
  biotoolsCURIE: biotools:bwasp
  biotoolsID: bwasp
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: vbrendel@indiana.edu
    fundrefid: null
    gridid: null
    name: Volker P. Brendel
    note: null
    orcidid: https://orcid.org/0000-0002-8055-7508
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Claire Morandin
    note: null
    orcidid: https://orcid.org/0000-0002-0811-901X
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: Tools and applications for integrative analysis of DNA methylation
    in social insects.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Methylation analysis
      uri: http://edamontology.org/operation_3204
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    - term: Sequence trimming
      uri: http://edamontology.org/operation_3192
    output: []
  homepage: https://BrendelGroup.org/SingularityHub/bwasp.sif
  homepage_status: 0
  language:
  - Shell
  - Perl
  - Python
  lastUpdate: '2021-12-12T14:42:49.498281Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/BrendelGroup/BWASP
  maturity: null
  name: BWASP
  operatingSystem: []
  otherID: []
  owner: Chan019
  publication:
  - doi: 10.1101/2021.08.19.457008
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Methylated DNA immunoprecipitation
    uri: http://edamontology.org/topic_3674
  - term: Epigenetics
    uri: http://edamontology.org/topic_3295
  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Microarray experiment
    uri: http://edamontology.org/topic_3518
  validated: 1
  version: []
- accessibility: null
  additionDate: '2021-09-27T07:24:13.280268Z'
  biotoolsCURIE: biotools:iblast
  biotoolsID: iblast
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: dashs@ornl.gov
    fundrefid: null
    gridid: null
    name: Sajal Dash
    note: null
    orcidid: https://orcid.org/0000-0001-5308-914X
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: feng@cs.vt.edu
    fundrefid: null
    gridid: null
    name: Wu-chun Feng
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: iBLAST is tool which performs incremental BLAST of new sequences via
    automated e-value correction.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output: []
  homepage: https://github.com/vtsynergy/iBLAST
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2021-09-27T07:24:13.284609Z'
  license: CC0-1.0
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/vtsynergy/iBLAST/issues
  maturity: null
  name: iBLAST
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1371/JOURNAL.PONE.0249410
    metadata:
      abstract: © 2021 Dash et al. This is an open access article distributed under
        the terms of the Creative Commons Attribution License, which permits unrestricted
        use, distribution, and reproduction in any medium, provided the original author
        and source are credited.Search results from local alignment search tools use
        statistical scores that are sensitive to the size of the database to report
        the quality of the result. For example, NCBI BLAST reports the best matches
        using similarity scores and expect values (i.e., e-values) calculated against
        the database size. Given the astronomical growth in genomics data throughout
        a genomic research investigation, sequence databases grow as new sequences
        are continuously being added to these databases. As a consequence, the results
        (e.g., best hits) and associated statistics (e.g., e-values) for a specific
        set of queries may change over the course of a genomic investigation. Thus,
        to update the results of a previously conducted BLAST search to find the best
        matches on an updated database, scientists must currently rerun the BLAST
        search against the entire updated database, which translates into irrecoverable
        and, in turn, wasted execution time, money, and computational resources. To
        address this issue, we devise a novel and efficient method to redeem past
        BLAST searches by introducing iBLAST. iBLAST leverages previous BLAST search
        results to conduct the same query search but only on the incremental (i.e.,
        newly added) part of the database, recomputes the associated critical statistics
        such as e-values, and combines these results to produce updated search results.
        Our experimental results and fidelity analyses show that iBLAST delivers search
        results that are identical to NCBI BLAST at a substantially reduced computational
        cost, i.e., iBLAST performs (1 + δ)/δ times faster than NCBI BLAST, where
        δ represents the fraction of database growth. We then present three different
        use cases to demonstrate that iBLAST can enable efficient biological discovery
        at a much faster speed with a substantially reduced computational cost.
      authors:
      - name: Dash S.
      - name: Rahman S.R.
      - name: Hines H.M.
      - name: Feng W.-C.
      citationCount: 0
      date: '2021-04-01T00:00:00Z'
      journal: PLoS ONE
      title: 'iBLAST: Incremental BLAST of new sequences via automated e-value correction'
    note: null
    pmcid: PMC8062096
    pmid: '33886589'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Biological databases
    uri: http://edamontology.org/topic_3071
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  validated: 0
  version: []
- accessibility: null
  additionDate: '2021-06-14T13:01:27Z'
  biotoolsCURIE: biotools:blast-qc
  biotoolsID: blast-qc
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: rsnorman@mailbox.sc.edu
    fundrefid: null
    gridid: null
    name: R. Sean Norman
    note: null
    orcidid: https://orcid.org/0000-0003-4766-4376
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: BLAST-QC is a tool for automated analysis of BLAST results.  It is
    a quality control filter and parser for NCBI BLAST XML results.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: Parsing
      uri: http://edamontology.org/operation_1812
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output: []
  homepage: https://github.com/torkian/blast-QC
  homepage_status: 0
  language:
  - C
  - Java
  - Python
  lastUpdate: '2021-08-18T08:27:48Z'
  license: MIT
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/torkian/blast-QC/issues
  maturity: null
  name: BLAST-QC
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1186/S40793-020-00361-Y
    metadata:
      abstract: '© 2020 The Author(s).Background: The Basic Local Alignment Search
        Tool (BLAST) from NCBI is the preferred utility for sequence alignment and
        identification for bioinformatics and genomics research. Among researchers
        using NCBI''s BLAST software, it is well known that analyzing the results
        of a large BLAST search can be tedious and time-consuming. Furthermore, with
        the recent discussions over the effects of parameters such as ''-max_target_seqs''
        on the BLAST heuristic search process, the use of these search options are
        questionable. This leaves using a stand-alone parser as one of the only options
        of condensing these large datasets, and with few available for download online,
        the task is left to the researcher to create a specialized piece of software
        anytime they need to analyze BLAST results. The need for a streamlined and
        fast script that solves these issues and can be easily implemented into a
        variety of bioinformatics and genomics workflows was the initial motivation
        for developing this software. Results: In this study, we demonstrate the effectiveness
        of BLAST-QC for analysis of BLAST results and its desirability over the other
        available options. Applying genetic sequence data from our bioinformatic workflows,
        we establish BLAST_QC''s superior runtime when compared to existing parsers
        developed with commonly used BioPerl and BioPython modules, as well as C and
        Java implementations of the BLAST_QC program. We discuss the ''max_target_seqs''
        parameter, the usage of and controversy around the use of the parameter, and
        offer a solution by demonstrating the ability of our software to provide the
        functionality this parameter was assumed to produce, as well as a variety
        of other parsing options. Executions of the script on example datasets are
        given, demonstrating the implemented functionality and providing test-cases
        of the program. BLAST-QC is designed to be integrated into existing software,
        and we establish its effectiveness as a module of workflows or other processes.
        Conclusions: BLAST-QC provides the community with a simple, lightweight and
        portable Python script that allows for easy quality control of BLAST results
        while avoiding the drawbacks of other options. This includes the uncertain
        results of applying the -max_target_seqs parameter or relying on the cumbersome
        dependencies of other options like BioPerl, Java, etc. which add complexity
        and run time when running large data sets of sequences. BLAST-QC is ideal
        for use in high-throughput workflows and pipelines common in bioinformatic
        and genomic research, and the script has been designed for portability and
        easy integration into whatever type of processes the user may be running.'
      authors:
      - name: Torkian B.
      - name: Hann S.
      - name: Preisner E.
      - name: Norman R.S.
      citationCount: 0
      date: '2020-08-12T00:00:00Z'
      journal: Environmental Microbiomes
      title: 'BLAST-QC: Automated analysis of BLAST results'
    note: null
    pmcid: PMC8066848
    pmid: '33902722'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Software engineering
    uri: http://edamontology.org/topic_3372
  validated: 0
  version: []
- accessibility: Open access (with restrictions)
  additionDate: '2021-05-26T19:30:25Z'
  biotoolsCURIE: biotools:blastkoala
  biotoolsID: blastkoala
  collectionID: []
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: kanehisa@kuicr.kyoto-u.ac.jp
    fundrefid: null
    gridid: null
    name: Minoru Kanehisa
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: BlastKOALA (KEGG Orthology And Links Annotation) is a KEGG Web service
    for annotating genomes and understanding organisms.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://www.kegg.jp/blastkoala/help_blastkoala.html
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    - term: Expression profile pathway mapping
      uri: http://edamontology.org/operation_0533
    output: []
  homepage: https://www.kegg.jp/blastkoala/
  homepage_status: 0
  language: []
  lastUpdate: '2021-06-25T09:09:16Z'
  license: null
  link: []
  maturity: null
  name: BlastKOALA
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1016/j.jmb.2015.11.006
    metadata:
      abstract: © 2015 The Authors.BlastKOALA and GhostKOALA are automatic annotation
        servers for genome and metagenome sequences, which perform KO (KEGG Orthology)
        assignments to characterize individual gene functions and reconstruct KEGG
        pathways, BRITE hierarchies and KEGG modules to infer high-level functions
        of the organism or the ecosystem. Both servers are made freely available at
        the KEGG Web site (http://www.kegg.jp/blastkoala/). In BlastKOALA, the KO
        assignment is performed by a modified version of the internally used KOALA
        algorithm after the BLAST search against a non-redundant dataset of pangenome
        sequences at the species, genus or family level, which is generated from the
        KEGG GENES database by retaining the KO content of each taxonomic category.
        In GhostKOALA, which utilizes more rapid GHOSTX for database search and is
        suitable for metagenome annotation, the pangenome dataset is supplemented
        with Cd-hit clusters including those for viral genes. The result files may
        be downloaded and manipulated for further KEGG Mapper analysis, such as comparative
        pathway analysis using multiple BlastKOALA results.
      authors:
      - name: Kanehisa M.
      - name: Sato Y.
      - name: Morishima K.
      citationCount: 948
      date: '2016-02-22T00:00:00Z'
      journal: Journal of Molecular Biology
      title: 'BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization
        of Genome and Metagenome Sequences'
    note: null
    pmcid: null
    pmid: '26585406'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  validated: 0
  version: []
- accessibility: null
  additionDate: '2017-12-18T00:03:48Z'
  biotoolsCURIE: biotools:bait
  biotoolsID: bait
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.terryfoxlab.ca/
  description: BAIT (Bioinformatic Analysis of Inherited Templates) is a software
    to create strand inheritance plots in data derived from the Strand-Seq sequencing
    protocol. The software is designed to be flexible with a range of species, and
    basic template folders can called to read in species-specific data.
  documentation:
  - note: null
    type:
    - General
    url: https://sourceforge.net/p/bait/wiki/Home/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Mapping
      uri: http://edamontology.org/operation_2429
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Analysis
      uri: http://edamontology.org/operation_2945
    output: []
  homepage: http://sourceforge.net/projects/bait/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2021-04-14T19:51:37Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: http://www.mybiosoftware.com/bait-1-0-organizing-genomes-and-mapping-rearrangements-in-single-cells.html
  maturity: null
  name: BAIT
  operatingSystem:
  - Linux
  otherID:
  - type: rrid
    value: RRID:SCR_000511
    version: null
  owner: mbs_import
  publication:
  - doi: 10.1038/nmeth.2206
    metadata:
      abstract: DNA rearrangements such as sister chromatid exchanges (SCEs) are sensitive
        indicators of genomic stress and instability, but they are typically masked
        by single-cell sequencing techniques. We developed Strand-seq to independently
        sequence parental DNA template strands from single cells, making it possible
        to map SCEs at orders-of-magnitude greater resolution than was previously
        possible. On average, murine embryonic stem (mES) cells exhibit eight SCEs,
        which are detected at a resolution of up to 23 bp. Strikingly, Strand-seq
        of 62 single mES cells predicts that the mm9 mouse reference genome assembly
        contains at least 17 incorrectly oriented segments totaling nearly 1% of the
        genome. These misoriented contigs and fragments have persisted through several
        iterations of the mouse reference genome and have been difficult to detect
        using conventional sequencing techniques. The ability to map SCE events at
        high resolution and fine-tune reference genomes by Strand-seq dramatically
        expands the scope of single-cell sequencing. © 2012 Nature America, Inc. All
        rights reserved.
      authors:
      - name: Falconer E.
      - name: Hills M.
      - name: Naumann U.
      - name: Poon S.S.S.
      - name: Chavez E.A.
      - name: Sanders A.D.
      - name: Zhao Y.
      - name: Hirst M.
      - name: Lansdorp P.M.
      citationCount: 74
      date: '2012-11-01T00:00:00Z'
      journal: Nature Methods
      title: DNA template strand sequencing of single-cells maps genomic rearrangements
        at high resolution
    note: null
    pmcid: PMC3580294
    pmid: '23042453'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
  - '1.4'
- accessibility: null
  additionDate: '2021-01-18T07:02:18Z'
  biotoolsCURIE: biotools:balas
  biotoolsID: balas
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: chris.wood@ed.ac.uk
    fundrefid: null
    gridid: null
    name: Christopher W Wood
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: r.sessions@bristol.ac.uk
    fundrefid: null
    gridid: null
    name: Richard B Sessions
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: BAlaS is an interactive web application for performing CASM via BudeAlaScan
    and visualizing its results. BAlaS is interactive and intuitive to use. Results
    are displayed directly in the browser for the structure being interrogated enabling
    their rapid inspection. BAlaS has broad applications in areas, such as drug discovery
    and protein-interface design.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Information extraction
      uri: http://edamontology.org/operation_3907
    - term: Protein structure validation
      uri: http://edamontology.org/operation_0321
    - term: Residue interaction calculation
      uri: http://edamontology.org/operation_0248
    output: []
  homepage: https://balas.app
  homepage_status: 0
  language:
  - Elm
  - Python
  - C++
  lastUpdate: '2021-03-11T14:55:26Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/wells-wood-research/balas
  maturity: null
  name: BAlaS
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1093/BIOINFORMATICS/BTAA026
    metadata:
      abstract: '© 2020 The Author(s). Published by Oxford University Press. All rights
        reserved.Motivation: In experimental protein engineering, alanine-scanning
        mutagenesis involves the replacement of selected residues with alanine to
        determine the energetic contribution of each side chain to forming an interaction.
        For example, it is often used to study protein-protein interactions. However,
        such experiments can be time-consuming and costly, which has led to the development
        of programmes for performing computational alanine-scanning mutagenesis (CASM)
        to guide experiments. While programmes are available for this, there is a
        need for a real-time web application that is accessible to non-expert users.
        Results: Here, we present BAlaS, an interactive web application for performing
        CASM via BudeAlaScan and visualizing its results. BAlaS is interactive and
        intuitive to use. Results are displayed directly in the browser for the structure
        being interrogated enabling their rapid inspection. BAlaS has broad applications
        in areas, such as drug discovery and protein-interface design.'
      authors:
      - name: Wood C.W.
      - name: Ibarra A.A.
      - name: Bartlett G.J.
      - name: Wilson A.J.
      - name: Wilson A.J.
      - name: Woolfson D.N.
      - name: Woolfson D.N.
      - name: Woolfson D.N.
      - name: Sessions R.B.
      - name: Sessions R.B.
      citationCount: 7
      date: '2020-05-01T00:00:00Z'
      journal: Bioinformatics
      title: 'BAlaS: Fast, interactive and accessible computational alanine-scanning
        using BudeAlaScan'
    note: null
    pmcid: null
    pmid: '31930404'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Protein interaction experiment
    uri: http://edamontology.org/topic_3957
  - term: Protein folding, stability and design
    uri: http://edamontology.org/topic_0130
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  validated: 0
  version: []
- accessibility: null
  additionDate: '2021-01-18T09:50:25Z'
  biotoolsCURIE: biotools:byase
  biotoolsID: byase
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: ghwang@hit.edu.cn
    fundrefid: null
    gridid: null
    name: Guohua Wang
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: BYASE is a Python package that uses Bayesian inference to identify
    gene-level and isoform-level ASE (Allele-specific expression) in polyploid (diploid
    or higher) organisms from single-end or paired-end RNA-seq data.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Phasing
      uri: http://edamontology.org/operation_3454
    - term: Differential gene expression analysis
      uri: http://edamontology.org/operation_3223
    - term: SNP annotation
      uri: http://edamontology.org/operation_3661
    output: []
  homepage: https://github.com/ncjllld/byase
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2021-02-06T20:44:11Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ncjllld/byase_gui
  maturity: null
  name: BYASE
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1093/BIOINFORMATICS/BTAA636
    metadata:
      abstract: '© 2020 Oxford University Press. All rights reserved.Allele-specific
        expression (ASE) is involved in many important biological mechanisms. We present
        a python package BYASE and its graphical user interface (GUI) tool BYASE-GUI
        for the identification of ASE from singleend and paired-end RNA-seq data based
        on Bayesian inference, which can simultaneously report differences in gene-level
        and isoform-level expression. BYASE uses both phased SNPs and non-phased SNPs,
        and supports polyploid organisms. Availability and implementation: The source
        codes of BYASE and BYASE-GUI are freely available at https://github. com/ncjllld/byase
        and https://github.com/ncjllld/byase_gui.'
      authors:
      - name: Dong L.
      - name: Wang J.
      - name: Wang G.
      citationCount: 0
      date: '2020-10-01T00:00:00Z'
      journal: Bioinformatics
      title: 'BYASE: A Python library for estimating gene and isoform level allele-specific
        expression'
    note: null
    pmcid: null
    pmid: '32678892'
    type: []
    version: null
  relation: []
  toolType:
  - Desktop application
  - Library
  topic:
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  - term: Epigenetics
    uri: http://edamontology.org/topic_3295
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  validated: 0
  version: []
- accessibility: null
  additionDate: '2021-01-18T09:16:14Z'
  biotoolsCURIE: biotools:blast2fish
  biotoolsID: blast2fish
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: mingwei@ntou.edu.tw
    fundrefid: null
    gridid: null
    name: Ming-Wei Lu
    note: null
    orcidid: https://orcid.org/0000-0003-3249-5311
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Blast2Fish is a reference-based annotation web tool for transcriptome
    analysis of non-model teleost fish. It is a novel approach for performing functional
    enrichment analysis on non-model teleost fish transcriptome data.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Gene-set enrichment analysis
      uri: http://edamontology.org/operation_2436
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Database search
      uri: http://edamontology.org/operation_2421
    - term: de Novo sequencing
      uri: http://edamontology.org/operation_3644
    - term: De-novo assembly
      uri: http://edamontology.org/operation_0524
    output: []
  homepage: http://blast2fish.ntou.edu.tw
  homepage_status: 0
  language: []
  lastUpdate: '2021-02-04T16:08:40Z'
  license: null
  link: []
  maturity: null
  name: Blast2Fish
  operatingSystem: []
  otherID: []
  owner: Kigaard
  publication:
  - doi: 10.1186/S12859-020-3507-9
    metadata:
      abstract: '© 2020 The Author(s).Background: Transcriptome analysis by next-generation
        sequencing has become a popular technique in recent years. This approach is
        quite suitable for non-model organism study, as de novo assembly is independent
        of prior genomic sequences of organisms. De novo sequencing has benefited
        many studies on commercially important fish species. However, to understand
        the functions of these assembled sequences, they still need to be annotated
        with existing sequence databases. By combining Basic Local Alignment Search
        Tool (BLAST) and Gene Ontology analysis, we were able to identify homologous
        sequences of assembled sequences and describe their characteristics using
        pre-defined tags for each gene, though the above conventional annotation results
        obtained for non-model assembled sequences was still associated with a lack
        of pre-defined tags and poorly documented records in the database. Results:
        We introduced Blast2Fish, a novel approach for performing functional enrichment
        analysis on non-model teleost fish transcriptome data. The Blast2Fish pipeline
        was designed to be a reference-based enrichment method. Instead of annotating
        the BLAST single top hit by a pre-defined gene-to-tag database, we included
        500 hits to search related PubMed articles and parse biological terms. These
        descriptive terms were then sorted and recorded as annotations for the query.
        The results showed that Blast2Fish was capable of providing meaningful annotations
        on immunology topics for non-model fish transcriptome analysis. Conclusion:
        Blast2Fish provides a novel approach for annotating sequences of non-model
        fish. The reference-based strategy allows annotation to be performed without
        pre-defined tags for each gene. This method strongly benefits non-model teleost
        fish studies for gene functional enrichment analysis.'
      authors:
      - name: Tso C.-H.
      - name: Wu J.-L.
      - name: Lu M.-W.
      citationCount: 2
      date: '2020-05-04T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'Blast2Fish: A reference-based annotation web tool for transcriptome
        analysis of non-model teleost fish'
    note: null
    pmcid: PMC7199347
    pmid: '32366294'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  validated: 0
  version: []
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