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      uri: http://edamontology.org/operation_0525
    output:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://cab.spbu.ru/software/spades/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2024-03-08T15:11:04.466129Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Galaxy service
    url: https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/spades/spades/3.9.0
  maturity: Mature
  name: SPAdes
  operatingSystem:
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  - Mac
  otherID: []
  owner: matus.kalas@uib.no
  publication:
  - doi: 10.1089/cmb.2012.0021
    metadata:
      abstract: The lion's share of bacteria in various environments cannot be cloned
        in the laboratory and thus cannot be sequenced using existing technologies.
        A major goal of single-cell genomics is to complement gene-centric metagenomic
        data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell
        data is challenging because of highly non-uniform read coverage as well as
        elevated levels of sequencing errors and chimeric reads. We describe SPAdes,
        a new assembler for both single-cell and standard (multicell) assembly, and
        demonstrate that it improves on the recently released E+V-SC assembler (specialized
        for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for
        multicell data). SPAdes generates single-cell assemblies, providing information
        about genomes of uncultivatable bacteria that vastly exceeds what may be obtained
        via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades).
        It is distributed as open source software. © Copyright 2012, Mary Ann Liebert,
        Inc.
      authors:
      - name: Bankevich A.
      - name: Nurk S.
      - name: Antipov D.
      - name: Gurevich A.A.
      - name: Dvorkin M.
      - name: Kulikov A.S.
      - name: Lesin V.M.
      - name: Nikolenko S.I.
      - name: Pham S.
      - name: Prjibelski A.D.
      - name: Pyshkin A.V.
      - name: Sirotkin A.V.
      - name: Vyahhi N.
      - name: Tesler G.
      - name: Alekseyev M.A.
      - name: Pevzner P.A.
      citationCount: 15962
      date: '2012-05-01T00:00:00Z'
      journal: Journal of Computational Biology
      title: 'SPAdes: A new genome assembly algorithm and its applications to single-cell
        sequencing'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.7490/f1000research.1114334.1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2016-12-19T14:28:27Z'
  biotoolsCURIE: biotools:cd-hit
  biotoolsID: cd-hit
  collectionID:
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  community: null
  confidence_flag: null
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  credit:
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    fundrefid: null
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    name: Galaxy Support Team
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: Cluster a nucleotide dataset into representative sequences.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/weizhongli/cdhit/wiki
  download: []
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    note: null
    operation:
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    output:
    - data:
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      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Data
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      format:
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        uri: http://edamontology.org/format_2330
    - data:
        term: Sequence alignment
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      - term: FASTA
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  homepage: https://github.com/weizhongli/cdhit
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2024-03-06T13:01:07.766440Z'
  license: null
  link:
  - note: null
    type:
    - Galaxy service
    url: https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/CD-HIT/4.6.1
  maturity: Mature
  name: cd-hit
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: hmenager
  publication:
  - doi: 10.1093/bioinformatics/bts565
    metadata: null
    note: null
    pmcid: PMC3516142
    pmid: '23060610'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btl158
    metadata: null
    note: null
    pmcid: null
    pmid: '16731699'
    type: []
    version: null
  - doi: 10.1093/bioinformatics/17.3.282
    metadata: null
    note: null
    pmcid: null
    pmid: '11294794'
    type: []
    version: null
  - doi: 10.1093/bioinformatics/18.1.77
    metadata: null
    note: null
    pmcid: null
    pmid: '11836214'
    type: []
    version: null
  - doi: 10.1093/bioinformatics/btq003
    metadata: null
    note: null
    pmcid: PMC2828112
    pmid: '20053844'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
  - 4.6.1
- accessibility: null
  additionDate: '2016-05-24T10:51:12Z'
  biotoolsCURIE: biotools:ribogalaxy
  biotoolsID: ribogalaxy
  collectionID: []
  community: null
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: info@sfi.ie
    fundrefid: null
    gridid: null
    name: Science Foundation Ireland
    note: null
    orcidid: null
    rorid: null
    typeEntity: Funding agency
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: ucc.ie
    note: null
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    typeEntity: Institute
    typeRole:
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    url: http://www.ucc.ie
  - email: ribogalaxy@gmail.com
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: http://ribogalaxy.ucc.ie/
  - email: p.baranov@ucc.ie
    fundrefid: null
    gridid: null
    name: Pavel V. Baranov
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: Galaxy-based web server where researchers can pre-process, align, analyze
    and visualize their own ribosome profiling (ribo-seq) data. GUI-based tools are
    provided to determine the strength of the triplet periodicity signal in ribo-seq
    data, generate metagene and ribosome profiles and carry out differential translation
    expression analysis using the riboSeqR suite. The RUST suite of tools can be used
    to quickly characterize ribosome profiling datasets to assess their quality and
    more.
  documentation:
  - note: null
    type:
    - Terms of use
    url: http://ribogalaxy.ucc.ie/static/conditions_of_use.html
  - note: null
    type:
    - General
    url: http://ribogalaxy.ucc.ie/
  download: []
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    type: private
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
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        term: Raw sequence
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      format:
      - term: FASTQ-sanger
        uri: http://edamontology.org/format_1932
    note: Raw ribo-seq and mRNA-seq FASTQ files There are multiple outputs depending
      on the tool/jobs that are run. Most of the ribo-seq analysis tools provide the
      output in both spreadsheet and/or visual format.
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Alignment
      uri: http://edamontology.org/operation_2928
    - term: Gene expression profiling
      uri: http://edamontology.org/operation_0314
    - term: Gene expression analysis
      uri: http://edamontology.org/operation_2495
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: bigWig
        uri: http://edamontology.org/format_3006
    - data:
        term: Sequence image
        uri: http://edamontology.org/data_2969
      format:
      - term: PNG
        uri: http://edamontology.org/format_3603
  homepage: http://ribogalaxy.ucc.ie
  homepage_status: 0
  language: []
  lastUpdate: '2024-02-23T09:02:01.891026Z'
  license: null
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/riboseqorg/RiboGalaxy
  maturity: Mature
  name: RiboGalaxy
  operatingSystem:
  - Windows
  - Mac
  otherID: []
  owner: A.Michel@ucc.ie
  publication:
  - doi: 10.1080/15476286.2016.1141862
    metadata:
      abstract: Ribosome profiling (ribo-seq) is a technique that uses high-throughput
        sequencing to reveal the exact locations and densities of translating ribosomes
        at the entire transcriptome level. The technique has become very popular since
        its inception in 2009. Yet experimentalists who generate ribo-seq data often
        have to rely on bioinformaticians to process and analyze their data. We present
        RiboGalaxy (http://ribogalaxy.ucc.ie), a freely available Galaxy-based web
        server for processing and analyzing ribosome profiling data with the visualization
        functionality provided by GWIPS-viz (http://gwips.ucc.ie). RiboGalaxy offers
        researchers a suite of tools specifically tailored for processing ribo-seq
        and corresponding mRNA-seq data. Researchers can take advantage of the published
        workflows which reduce the multi-step alignment process to a minimum of inputs
        from the user. Users can then explore their own aligned data as custom tracks
        in GWIPS-viz and compare their ribosome profiles to existing ribo-seq tracks
        from published studies. In addition, users can assess the quality of their
        ribo-seq data, determine the strength of the triplet periodicity signal, generate
        meta-gene ribosome profiles as well as analyze the relative impact of mRNA
        sequence features on local read density. RiboGalaxy is accompanied by extensive
        documentation and tips for helping users. In addition we provide a forum (http://gwips.ucc.ie/Forum)
        where we encourage users to post their questions and feedback to improve the
        overall RiboGalaxy service.
      authors:
      - name: Michel A.M.
      - name: Mullan J.P.A.
      - name: Velayudhan V.
      - name: O'Connor P.B.F.
      - name: Donohue C.A.
      - name: Baranov P.V.
      citationCount: 67
      date: '2016-03-03T00:00:00Z'
      journal: RNA Biology
      title: 'RiboGalaxy: A browser based platform for the alignment, analysis and
        visualization of ribosome profiling data'
    note: null
    pmcid: PMC4829337
    pmid: '26821742'
    type:
    - Primary
    version: null
  - doi: 10.1016/J.JMB.2023.168043
    metadata:
      abstract: Ribosome profiling (Ribo-Seq) captures a “snapshot” of ribosomes’
        locations at the entire transcriptome of a cell at sub-codon resolution providing
        insights into gene expression and enabling the discovery of novel translated
        regions. RiboGalaxy (https://ribogalaxy.genomicsdatascience.ie/), a Galaxy-based
        platform for processing Ribo-Seq data is a RiboSeq.Org (https://riboseq.org/)
        resource. RiboSeq.Org is an online gateway to a set of integrated tools for
        the processing and analysis of Ribo-Seq data. In this RiboGalaxy update we
        introduce changes to both the tools available on RiboGalaxy and to how the
        resource is managed on the backend. For example, in order to improve interoperability
        between Riboseq.Org resources, we added tools that link RiboGalaxy outputs
        with Trips-Viz and GWIPS-viz browsers for downstream analysis and visualisation.
        RiboGalaxy's backend now utilises Ansible configuration management which enhances
        its stability and jobs are executed within Singularity containers and are
        managed by Slurm, strengthening reproducibility and performance respectively.
      authors:
      - name: Fedorova A.D.
      - name: Tierney J.A.S.
      - name: Michel A.M.
      - name: Baranov P.V.
      citationCount: 1
      date: '2023-07-15T00:00:00Z'
      journal: Journal of Molecular Biology
      title: 'RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data
        Processing – 2023 Update'
    note: null
    pmcid: null
    pmid: '37356899'
    type:
    - Review
    version: null
  relation: []
  toolType:
  - Workbench
  topic:
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2022-11-03T15:52:41.693905Z'
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  biotoolsID: hmmer_hmmscan_ebi
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  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Sean Eddy
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: EMBL-EBI
    note: null
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    rorid: null
    typeEntity: Institute
    typeRole:
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    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: HMMER3 hmmscan is used to search sequences against collections of profiles.
  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: http://hmmer.org/
  download:
  - note: null
    type: Downloads page
    url: http://hmmer.org/
    version: null
  editPermission:
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  function:
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    input:
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      format: []
    - data:
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        uri: http://edamontology.org/data_1364
      format: []
    note: null
    operation:
    - term: Sequence database search
      uri: http://edamontology.org/operation_0338
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: Database hits (sequence) format
        uri: http://edamontology.org/format_2066
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format: []
  homepage: https://www.ebi.ac.uk/jdispatcher/pfa/hmmer3_hmmscan
  homepage_status: 0
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  lastUpdate: '2024-02-08T10:58:38.007948Z'
  license: null
  link:
  - note: null
    type:
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    url: https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services
  maturity: null
  name: HMMER hmmscan (EBI)
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: jdispatcher
  publication:
  - doi: 10.1093/nar/gkr367
    metadata:
      abstract: HMMER is a software suite for protein sequence similarity searches
        using probabilistic methods. Previously, HMMER has mainly been available only
        as a computationally intensive UNIX command-line tool, restricting its use.
        Recent advances in the software, HMMER3, have resulted in a 100-fold speed
        gain relative to previous versions. It is now feasible to make efficient profile
        hidden Markov model (profile HMM) searches via the web. A HMMER web server
        (http://hmmer.janelia.org) has been designed and implemented such that most
        protein database searches return within a few seconds. Methods are available
        for searching either a single protein sequence, multiple protein sequence
        alignment or profile HMM against a target sequence database, and for searching
        a protein sequence against Pfam. The web server is designed to cater to a
        range of different user expertise and accepts batch uploading of multiple
        queries at once. All search methods are also available as RESTful web services,
        thereby allowing them to be readily integrated as remotely executed tasks
        in locally scripted workflows. We have focused on minimizing search times
        and the ability to rapidly display tabular results, regardless of the number
        of matches found, developing graphical summaries of the search results to
        provide quick, intuitive appraisement of them. © 2011 The Author(s).
      authors:
      - name: Finn R.D.
      - name: Clements J.
      - name: Eddy S.R.
      citationCount: 3538
      date: '2011-07-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'HMMER web server: Interactive sequence similarity searching'
    note: null
    pmcid: null
    pmid: null
    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: 699
      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: hmmer3
    type: uses
  toolType:
  - Web application
  - Web service
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  validated: 0
  version:
  - '1'
- accessibility: null
  additionDate: '2022-11-03T15:52:37.739953Z'
  biotoolsCURIE: biotools:hmmer_phmmer_ebi
  biotoolsID: hmmer_phmmer_ebi
  collectionID:
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  - Job Dispatcher Tools
  community: null
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Sean Eddy
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: EMBL-EBI
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    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: HMMER3 phmmer is used to search one or more sequences against a sequence
    database.
  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: http://hmmer.org/
  download:
  - note: null
    type: Downloads page
    url: http://hmmer.org/
    version: null
  editPermission:
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  elixir_badge: 0
  function:
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    input:
    - data:
        term: Sequence record
        uri: http://edamontology.org/data_0849
      format: []
    - data:
        term: Hidden Markov model
        uri: http://edamontology.org/data_1364
      format: []
    note: null
    operation:
    - term: Sequence database search
      uri: http://edamontology.org/operation_0338
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: Database hits (sequence) format
        uri: http://edamontology.org/format_2066
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format: []
  homepage: https://www.ebi.ac.uk/jdispatcher/pfa/hmmer3_phmmer
  homepage_status: 0
  language: []
  lastUpdate: '2024-02-08T10:54:28.651795Z'
  license: null
  link:
  - note: null
    type:
    - Helpdesk
    url: https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services
  maturity: null
  name: HMMER phmmer (EBI)
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: jdispatcher
  publication:
  - doi: 10.1093/nar/gkr367
    metadata:
      abstract: HMMER is a software suite for protein sequence similarity searches
        using probabilistic methods. Previously, HMMER has mainly been available only
        as a computationally intensive UNIX command-line tool, restricting its use.
        Recent advances in the software, HMMER3, have resulted in a 100-fold speed
        gain relative to previous versions. It is now feasible to make efficient profile
        hidden Markov model (profile HMM) searches via the web. A HMMER web server
        (http://hmmer.janelia.org) has been designed and implemented such that most
        protein database searches return within a few seconds. Methods are available
        for searching either a single protein sequence, multiple protein sequence
        alignment or profile HMM against a target sequence database, and for searching
        a protein sequence against Pfam. The web server is designed to cater to a
        range of different user expertise and accepts batch uploading of multiple
        queries at once. All search methods are also available as RESTful web services,
        thereby allowing them to be readily integrated as remotely executed tasks
        in locally scripted workflows. We have focused on minimizing search times
        and the ability to rapidly display tabular results, regardless of the number
        of matches found, developing graphical summaries of the search results to
        provide quick, intuitive appraisement of them. © 2011 The Author(s).
      authors:
      - name: Finn R.D.
      - name: Clements J.
      - name: Eddy S.R.
      citationCount: 3538
      date: '2011-07-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'HMMER web server: Interactive sequence similarity searching'
    note: null
    pmcid: null
    pmid: null
    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: 699
      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: hmmer3
    type: uses
  toolType:
  - Web application
  - Web service
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  validated: 0
  version:
  - '1'
- accessibility: null
  additionDate: '2015-01-29T15:46:55Z'
  biotoolsCURIE: biotools:seqret-ebi
  biotoolsID: seqret-ebi
  collectionID:
  - EMBOSS at EBI Tools
  - EBI Tools
  - Job Dispatcher Tools
  community: null
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: EMBOSS
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - 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: Job Dispatcher
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Primary contact
    url: https://www.ebi.ac.uk/jdispatcher
  description: Sequence format coversion tool.
  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://emboss.sourceforge.net/
  download:
  - note: null
    type: Downloads page
    url: https://emboss.sourceforge.net/
    version: null
  editPermission:
    authors:
    - biomadeira
    - nandana
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format: []
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Formatting
      uri: http://edamontology.org/operation_0335
    output:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format: []
  homepage: https://www.ebi.ac.uk/jdispatcher/sfc/emboss_seqret
  homepage_status: 0
  language: []
  lastUpdate: '2024-02-05T19:37:50.317443Z'
  license: null
  link:
  - note: null
    type:
    - Helpdesk
    url: https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services
  maturity: null
  name: seqret (EBI)
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: jdispatcher
  publication:
  - doi: 10.1016/S0168-9525(00)02024-2
    metadata:
      abstract: ''
      authors:
      - name: Rice P.
      - name: Longden L.
      - name: Bleasby A.
      citationCount: 6810
      date: '2000-06-01T00:00:00Z'
      journal: Trends in Genetics
      title: 'EMBOSS: The European Molecular Biology Open Software Suite'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkac240
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation:
  - biotoolsID: seqret
    type: uses
  toolType:
  - Web application
  - Web service
  topic:
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 1
  version:
  - '1'
- accessibility: null
  additionDate: '2015-01-29T15:46:49Z'
  biotoolsCURIE: biotools:mview_ebi
  biotoolsID: mview_ebi
  collectionID:
  - EBI Tools
  - Job Dispatcher Tools
  community: null
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Nigel Brown
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - 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: Job Dispatcher
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Primary contact
    url: https://www.ebi.ac.uk/jdispatcher
  description: Reformat the results of a sequence database search (BLAST, FASTA) or
    a multiple alignment adding optional HTML markup to control colouring and web
    page layout.
  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://desmid.github.io/mview/
  download:
  - note: null
    type: Downloads page
    url: https://desmid.github.io/mview/
    version: null
  editPermission:
    authors:
    - biomadeira
    - nandana
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    note: null
    operation:
    - term: Formatting
      uri: http://edamontology.org/operation_0335
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format: []
  homepage: https://www.ebi.ac.uk/jdispatcher/msa/mview
  homepage_status: 0
  language: []
  lastUpdate: '2024-02-05T19:13:29.787255Z'
  license: null
  link:
  - note: null
    type:
    - Helpdesk
    url: https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services
  maturity: null
  name: MView (EBI)
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: jdispatcher
  publication:
  - doi: 10.1093/bioinformatics/14.4.380
    metadata:
      abstract: 'Summary: MView is a tool for converting the results of a sequence
        database search into the form of a coloured multiple alignment of hits stacked
        against the query. Alternatively, an existing multiple alignment can be processed.
        In either case, the output is simply HTML, so the result is platform independent
        and does not require a separate application or applet to be loaded. Availability:
        Free from http://www.sander.ebi.ac.uk/mview/ subject to copyright restrictions.
        Contact: brown@@@ebi.ac.uk.'
      authors:
      - name: Brown N.P.
      - name: Leroy C.
      - name: Sander C.
      citationCount: 282
      date: '1998-01-01T00:00:00Z'
      journal: Bioinformatics
      title: 'MView: A web-compatible database search or multiple alignment viewer'
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkac240
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web application
  - Web service
  topic:
  - term: Data management
    uri: http://edamontology.org/topic_3071
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 1
  version:
  - '1'
next: ?page=2
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