count: 68
list:
- accessibility: Open access
  additionDate: '2024-03-06T10:49:13.850578Z'
  biotoolsCURIE: biotools:maast
  biotoolsID: maast
  collectionID: []
  community: null
  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: '2024-03-06T10:49:13.853528Z'
  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: 0
      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
  community: null
  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:
    - biomadeira
    - sergitobara
    - nandana
    type: group
  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: https://www.ebi.ac.uk/jdispatcher/sss/ncbiblast
  homepage_status: 0
  language: []
  lastUpdate: '2024-01-12T16:24:54.401987Z'
  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: 10984
      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/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: 651
      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: null
    pmid: null
    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: Open access
  additionDate: '2024-01-03T21:43:37.162391Z'
  biotoolsCURIE: biotools:flust
  biotoolsID: flust
  collectionID: []
  community: null
  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: '2024-01-03T21:43:37.165389Z'
  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: 0
      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: null
  additionDate: '2017-01-13T13:16:01Z'
  biotoolsCURIE: biotools:quast
  biotoolsID: quast
  collectionID: []
  community: null
  confidence_flag: null
  cost: null
  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
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    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: '2023-11-02T09:05:55.519354Z'
  license: GPL-2.0
  link: []
  maturity: Mature
  name: QUAST
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: null
    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: 2607
      date: '2013-04-15T00:00:00Z'
      journal: Bioinformatics
      title: 'QUAST: Quality assessment tool for genome assemblies'
    note: null
    pmcid: null
    pmid: '23422339'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2023-10-15T19:46:30.952186Z'
  biotoolsCURIE: biotools:blaze
  biotoolsID: blaze
  collectionID: []
  community: null
  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: '2023-10-15T19:46:30.954920Z'
  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: 2
      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: null
  additionDate: '2021-05-26T19:33:15Z'
  biotoolsCURIE: biotools:boost
  biotoolsID: boost
  collectionID: []
  community: null
  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:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  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
  community: null
  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: '2017-01-13T13:13:50Z'
  biotoolsCURIE: biotools:blast
  biotoolsID: blast
  collectionID:
  - BLAST
  community: null
  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: '2022-07-15T15:52:20.300974Z'
  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: 67988
      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: '© 2016 The Author 2016. Published by Oxford University Press.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: 6
      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: 1931
      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: 579
      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: null
  additionDate: '2017-03-01T15:34:10Z'
  biotoolsCURIE: biotools:blast2go
  biotoolsID: blast2go
  collectionID:
  - BLAST
  community: null
  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: '2022-06-27T14:51:01.924474Z'
  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: 8122
      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: 2670
      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: null
  additionDate: '2017-01-17T15:07:46Z'
  biotoolsCURIE: biotools:beast
  biotoolsID: beast
  collectionID:
  - EBI Training Tools
  community: null
  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: []
  elixirPlatform: []
  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: '2022-06-21T13:21:16.387963Z'
  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: 7434
      date: '2012-08-01T00:00:00Z'
      journal: Molecular Biology and Evolution
      title: Bayesian phylogenetics with BEAUti and the BEAST 1.7
    note: null
    pmcid: null
    pmid: null
    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: 9741
      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: []
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