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In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1348, "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." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "hmenager", "additionDate": "2016-12-19T14:26:26Z", "lastUpdate": "2024-03-08T15:26:38.619142Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SPAdes", "description": "St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.", "homepage": "http://cab.spbu.ru/software/spades/", "biotoolsID": "spades", "biotoolsCURIE": "biotools:spades", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0525", "term": "Genome assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-2.0", "collectionID": [ "SPAdes", "galaxyPasteur", "Animal and Crop Genomics" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/spades/spades/3.9.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "http://cab.spbu.ru/files/release3.10.1/manual.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1089/cmb.2012.0021", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing", "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.", "date": "2012-05-01T00:00:00Z", "citationCount": 15962, "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." } ], "journal": "Journal of Computational Biology" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": null, "email": "spades.support@cab.spbu.ru", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "matus.kalas@uib.no", "additionDate": "2017-08-20T17:30:35Z", "lastUpdate": "2024-03-08T15:11:04.466129Z", "editPermission": { "type": "public", "authors": [ "animalandcropgenomics", "alexcorm" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "cd-hit", "description": "Cluster a nucleotide dataset into representative sequences.", "homepage": "https://github.com/weizhongli/cdhit", "biotoolsID": "cd-hit", "biotoolsCURIE": "biotools:cd-hit", "version": [ "4.6.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0291", "term": "Sequence clustering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C++" ], "license": null, "collectionID": [ "galaxyPasteur" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/CD-HIT/4.6.1", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/weizhongli/cdhit/wiki", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bts565", "pmid": "23060610", "pmcid": "PMC3516142", "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/btl158", "pmid": "16731699", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/17.3.282", "pmid": "11294794", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/18.1.77", "pmid": "11836214", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/bioinformatics/btq003", "pmid": "20053844", "pmcid": "PMC2828112", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "hmenager", "additionDate": "2016-12-19T14:28:27Z", "lastUpdate": "2024-03-06T13:01:07.766440Z", "editPermission": { "type": "group", "authors": [ "sergitobara", "ELIXIR-CZ", "yaominmin" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RiboGalaxy", "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.", "homepage": "http://ribogalaxy.ucc.ie", "biotoolsID": "ribogalaxy", "biotoolsCURIE": "biotools:ribogalaxy", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" }, { "uri": "http://edamontology.org/operation_2495", "term": "Gene expression analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0848", "term": "Raw sequence" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3006", "term": "bigWig" } ] }, { "data": { "uri": "http://edamontology.org/data_2969", "term": "Sequence image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] } ], "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.", "cmd": null } ], "toolType": [ "Workbench" ], "topic": [ { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" } ], "operatingSystem": [ "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [ "Galaxy" ], "link": [ { "url": "https://github.com/riboseqorg/RiboGalaxy", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "http://ribogalaxy.ucc.ie/static/conditions_of_use.html", "type": [ "Terms of use" ], "note": null }, { "url": "http://ribogalaxy.ucc.ie/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1080/15476286.2016.1141862", "pmid": "26821742", "pmcid": "PMC4829337", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data", "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.", "date": "2016-03-03T00:00:00Z", "citationCount": 67, "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." } ], "journal": "RNA Biology" } }, { "doi": "10.1016/J.JMB.2023.168043", "pmid": "37356899", "pmcid": null, "type": [ "Review" ], "version": null, "note": null, "metadata": { "title": "RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing – 2023 Update", "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.", "date": "2023-07-15T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Fedorova A.D." }, { "name": "Tierney J.A.S." }, { "name": "Michel A.M." }, { "name": "Baranov P.V." } ], "journal": "Journal of Molecular Biology" } } ], "credit": [ { "name": "Science Foundation Ireland", "email": "info@sfi.ie", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "ucc.ie", "email": null, "url": "http://www.ucc.ie", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "ribogalaxy@gmail.com", "url": "http://ribogalaxy.ucc.ie/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Pavel V. Baranov", "email": "p.baranov@ucc.ie", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "A.Michel@ucc.ie", "additionDate": "2016-05-24T10:51:12Z", "lastUpdate": "2024-02-23T09:02:01.891026Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bowtie 2", "description": "Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.", "homepage": "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml", "biotoolsID": "bowtie2", "biotoolsCURIE": "biotools:bowtie2", "version": [], "otherID": [ { "value": "RRID:SCR_016368", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" } ], "operatingSystem": [ "Linux" ], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [ "galaxyPasteur" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/bowtie2/bowtie2/2.2.6.2", "type": [ "Galaxy service" ], "note": null } ], "download": [ { "url": "https://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/bowtie2.cwl", "type": "Tool wrapper (CWL)", "note": null, "version": null }, { "url": "https://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/bowtie2_build.cwl", "type": "Tool wrapper (CWL)", "note": null, "version": null }, { "url": "https://docker-ui.genouest.org/app/#/container/bioconda/bowtie2", "type": "Container file", "note": null, "version": null }, { "url": "https://anaconda.org/bioconda/bowtie2", "type": "Container file", "note": null, "version": null }, { "url": "https://tracker.debian.org/pkg/bowtie2", "type": "Software package", "note": "Link to the Debian package information. This form of the link is recommended by the Debian devs & Med team, and in the future all this information, including versions, will be pushed to GitHub automatically (matuskalas)", "version": "2.2.4-1, 2.3.0-2, 2.3.4.3-1, 2.3.5.1-1, 2.3.5.1-1" }, { "url": "https://bioconda.github.io/recipes/bowtie2/README.html", "type": "Software package", "note": "Link to the Bioconda package information. This form of the link is recommended by the Bioconda team, and in the future all this information, including versions (limit 100 chars), will be pushed to GitHub automatically (matuskalas)", "version": "2.3.5-0, 2.3.4.3-1 - 2.3.0-0, 2.2.8-2 - 2.2.1-0" } ], "documentation": [ { "url": "http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml", "type": [ "User manual" ], "note": null }, { "url": "https://github.com/BenLangmead/bowtie2", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/nmeth.1923", "pmid": "22388286", "pmcid": "PMC3322381", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Fast gapped-read alignment with Bowtie 2", "abstract": "As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy. © 2012 Nature America, Inc. All rights reserved.", "date": "2012-04-01T00:00:00Z", "citationCount": 18223, "authors": [ { "name": "Langmead B." }, { "name": "Salzberg S.L." } ], "journal": "Nature Methods" } }, { "doi": "10.1186/1471-2105-14-184", "pmid": "23758764", "pmcid": "PMC3694458", "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Benchmarking short sequence mapping tools", "abstract": "Background: The development of next-generation sequencing instruments has led to the generation of millions of short sequences in a single run. The process of aligning these reads to a reference genome is time consuming and demands the development of fast and accurate alignment tools. However, the current proposed tools make different compromises between the accuracy and the speed of mapping. Moreover, many important aspects are overlooked while comparing the performance of a newly developed tool to the state of the art. Therefore, there is a need for an objective evaluation method that covers all the aspects. In this work, we introduce a benchmarking suite to extensively analyze sequencing tools with respect to various aspects and provide an objective comparison.Results: We applied our benchmarking tests on 9 well known mapping tools, namely, Bowtie, Bowtie2, BWA, SOAP2, MAQ, RMAP, GSNAP, Novoalign, and mrsFAST (mrFAST) using synthetic data and real RNA-Seq data. MAQ and RMAP are based on building hash tables for the reads, whereas the remaining tools are based on indexing the reference genome. The benchmarking tests reveal the strengths and weaknesses of each tool. The results show that no single tool outperforms all others in all metrics. However, Bowtie maintained the best throughput for most of the tests while BWA performed better for longer read lengths. The benchmarking tests are not restricted to the mentioned tools and can be further applied to others.Conclusion: The mapping process is still a hard problem that is affected by many factors. In this work, we provided a benchmarking suite that reveals and evaluates the different factors affecting the mapping process. Still, there is no tool that outperforms all of the others in all the tests. Therefore, the end user should clearly specify his needs in order to choose the tool that provides the best results. © 2013 Hatem et al.; licensee BioMed Central Ltd.", "date": "2013-06-07T00:00:00Z", "citationCount": 121, "authors": [ { "name": "Hatem A." }, { "name": "Bozdag D." }, { "name": "Toland A.E." }, { "name": "Catalyurek U.V." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1016/j.ygeno.2017.03.001", "pmid": "28286147", "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics", "abstract": "© 2017 Elsevier Inc.Massive data produced due to the advent of next-generation sequencing (NGS) technology is widely used for biological researches and medical diagnosis. The crucial step in NGS analysis is read alignment or mapping which is computationally intensive and complex. The mapping bias tends to affect the downstream analysis, including detection of polymorphisms. In order to provide guidelines to the biologist for suitable selection of aligners; we have evaluated and benchmarked 5 different aligners (BWA, Bowtie2, NovoAlign, Smalt and Stampy) and their mapping bias based on characteristics of 5 microbial genomes. Two million simulated read pairs of various sizes (36 bp, 50 bp, 72 bp, 100 bp, 125 bp, 150 bp, 200 bp, 250 bp and 300 bp) were aligned. Specific alignment features such as sensitivity of mapping, percentage of properly paired reads, alignment time and effect of tandem repeats on incorrectly mapped reads were evaluated. BWA showed faster alignment followed by Bowtie2 and Smalt. NovoAlign and Stampy were comparatively slower. Most of the aligners showed high sensitivity towards long reads (> 100 bp) mapping. On the other hand NovoAlign showed higher sensitivity towards both short reads (36 bp, 50 bp, 72 bp) and long reads (> 100 bp) mappings; It also showed higher sensitivity towards mapping a complex genome like Plasmodium falciparum. The percentage of properly paired reads aligned by NovoAlign, BWA and Stampy were markedly higher. None of the aligners outperforms the others in the benchmark, however the aligners perform differently with genome characteristics. We expect that the results from this study will be useful for the end user to choose aligner, thus enhance the accuracy of read mapping.", "date": "2017-07-01T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Thankaswamy-Kosalai S." }, { "name": "Sen P." }, { "name": "Nookaew I." } ], "journal": "Genomics" } }, { "doi": "10.1186/1471-2164-15-264", "pmid": "24708189", "pmcid": "PMC4051166", "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Comparison of mapping algorithms used in high-throughput sequencing: Application to Ion Torrent data", "abstract": "Background: The rapid evolution in high-throughput sequencing (HTS) technologies has opened up new perspectives in several research fields and led to the production of large volumes of sequence data. A fundamental step in HTS data analysis is the mapping of reads onto reference sequences. Choosing a suitable mapper for a given technology and a given application is a subtle task because of the difficulty of evaluating mapping algorithms.Results: In this paper, we present a benchmark procedure to compare mapping algorithms used in HTS using both real and simulated datasets and considering four evaluation criteria: computational resource and time requirements, robustness of mapping, ability to report positions for reads in repetitive regions, and ability to retrieve true genetic variation positions. To measure robustness, we introduced a new definition for a correctly mapped read taking into account not only the expected start position of the read but also the end position and the number of indels and substitutions. We developed CuReSim, a new read simulator, that is able to generate customized benchmark data for any kind of HTS technology by adjusting parameters to the error types. CuReSim and CuReSimEval, a tool to evaluate the mapping quality of the CuReSim simulated reads, are freely available. We applied our benchmark procedure to evaluate 14 mappers in the context of whole genome sequencing of small genomes with Ion Torrent data for which such a comparison has not yet been established.Conclusions: A benchmark procedure to compare HTS data mappers is introduced with a new definition for the mapping correctness as well as tools to generate simulated reads and evaluate mapping quality. The application of this procedure to Ion Torrent data from the whole genome sequencing of small genomes has allowed us to validate our benchmark procedure and demonstrate that it is helpful for selecting a mapper based on the intended application, questions to be addressed, and the technology used. This benchmark procedure can be used to evaluate existing or in-development mappers as well as to optimize parameters of a chosen mapper for any application and any sequencing platform. © 2014 Caboche et al.; licensee BioMed Central Ltd.", "date": "2014-04-05T00:00:00Z", "citationCount": 55, "authors": [ { "name": "Caboche S." }, { "name": "Audebert C." }, { "name": "Lemoine Y." }, { "name": "Hot D." } ], "journal": "BMC Genomics" } }, { "doi": "10.1093/bioinformatics/btu146", "pmid": "24626854", "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Lacking alignments? The next-generation sequencing mapper segemehl revisited", "abstract": "Motivation: Next-generation sequencing has become an important tool in molecular biology. Various protocols to investigate genomic, transcriptomic and epigenomic features across virtually all species and tissues have been devised. For most of these experiments, one of the first crucial steps of bioinformatic analysis is the mapping of reads to reference genomes. Results: Here, we present thorough benchmarks of our read aligner segemehl in comparison with other state-of-the-art methods. Furthermore, we introduce the tool lack to rescue unmapped RNA-seq reads which works in conjunction with segemehl and many other frequently used split-read aligners. © The Author 2014.", "date": "2014-07-01T00:00:00Z", "citationCount": 46, "authors": [ { "name": "Otto C." }, { "name": "Stadler P.F." }, { "name": "Hoffmann S." } ], "journal": "Bioinformatics" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Institut Français de Bioinformatique", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Ben Langmead", "email": null, "url": "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Ben Langmead", "email": null, "url": "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "swohlgemuth", "additionDate": "2016-03-24T16:39:49Z", "lastUpdate": "2024-02-16T10:45:32.677126Z", "editPermission": { "type": "group", "authors": [ "swohlgemuth", "rioualen" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GPCRDB", "description": "GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs). GPCRdb curates sequence alignments, structures and receptor mutations from literature. Interactive diagrams visualise receptor residues (e.g. snakeplot and helix box plot) and relationships (e.g phylogenetic trees).", "homepage": "https://gpcrdb.org", "biotoolsID": "gpcrdb", "biotoolsCURIE": "biotools:gpcrdb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" }, { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2451", "term": "Sequence comparison" }, { "uri": "http://edamontology.org/operation_0240", "term": "Sequence motif comparison" }, { "uri": "http://edamontology.org/operation_0291", "term": "Sequence clustering" }, { "uri": "http://edamontology.org/operation_2990", "term": "Classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1381", "term": "Sequence alignment (pair)" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1707", "term": "Phylogenetic tree image" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3542", "term": "Protein secondary structure" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_3534", "term": "Protein binding sites" }, { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" }, { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python", "SQL" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/protwis/protwis", "type": [ "Repository" ], "note": "Source of the framework that runs GPCRdb" }, { "url": "https://github.com/protwis/gpcrdb_data", "type": [ "Repository" ], "note": "Data repository for the GPCRdb" }, { "url": "https://github.com/protwis/protwis/issues", "type": [ "Issue tracker" ], "note": "Issue tracker for the GPCRdb" } ], "download": [], "documentation": [ { "url": "https://docs.gpcrdb.org", "type": [ "General" ], "note": "Documentation of the GPCRdb ranging from a general introduction to tool descriptions and development instructions." }, { "url": "https://gpcrdb.org/services/reference/", "type": [ "API documentation" ], "note": "Documentation for the REST web services" } ], "publication": [ { "doi": "10.1093/nar/gkv1178", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "2016 GPCRdb publication", "metadata": { "title": "GPCRdb: An information system for G protein-coupled receptors", "abstract": "© The Author(s) 2015.Recent developments in G protein-coupled receptor (GPCR) structural biology and pharmacology have greatly enhanced our knowledge of receptor structure-function relations, and have helped improve the scientific foundation for drug design studies. The GPCR database, GPCRdb, serves a dual role in disseminating and enabling new scientific developments by providing reference data, analysis tools and interactive diagrams. This paper highlights new features in the fifth major GPCRdb release: (i) GPCR crystal structure browsing, superposition and display of ligand interactions; (ii) direct deposition by users of point mutations and their effects on ligand binding; (iii) refined snake and helix box residue diagram looks; and (iii) phylogenetic trees with receptor classification colour schemes. Under the hood, the entire GPCRdb front- and back-ends have been recoded within one infrastructure, ensuring a smooth browsing experience and development. GPCRdb is available at http://www.gpcrdb.org/ and it's open source code at https://bitbucket.org/gpcr/protwis.", "date": "2016-01-01T00:00:00Z", "citationCount": 196, "authors": [ { "name": "Isberg V." }, { "name": "Mordalski S." }, { "name": "Munk C." }, { "name": "Rataj K." }, { "name": "Harpsoe K." }, { "name": "Hauser A.S." }, { "name": "Vroling B." }, { "name": "Bojarski A.J." }, { "name": "Vriend G." }, { "name": "Gloriam D.E." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkaa1080", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": "2021 GPCRdb publication", "metadata": { "title": "GPCRdb in 2021: Integrating GPCR sequence, structure and function", "abstract": "© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.G protein-coupled receptors (GPCRs) form both the largest family of membrane proteins and drug targets, mediating the action of one-third of medicines. The GPCR database, GPCRdb serves >4 000 researchers every month and offers reference data, analysis of own or literature data, experiment design and dissemination of published datasets. Here, we describe new and updated GPCRdb resources with a particular focus on integration of sequence, structure and function. GPCRdb contains all human non-olfactory GPCRs (and >27 000 orthologs), G-proteins and arrestins. It includes over 2 000 drug and in-trial agents and nearly 200 000 ligands with activity and availability data. GPCRdb annotates all published GPCR structures (updated monthly), which are also offered in a refined version (with re-modeled missing/distorted regions and reverted mutations) and provides structure models of all human non-olfactory receptors in inactive, intermediate and active states. Mutagenesis data in the GPCRdb spans natural genetic variants, GPCR-G protein interfaces, ligand sites and thermostabilising mutations. A new sequence signature tool for identification of functional residue determinants has been added and two data driven tools to design ligand site mutations and constructs for structure determination have been updated extending their coverage of receptors and modifications. The GPCRdb is available at https://gpcrdb.org.", "date": "2021-01-08T00:00:00Z", "citationCount": 129, "authors": [ { "name": "Kooistra A.J." }, { "name": "Mordalski S." }, { "name": "Pandy-Szekeres G." }, { "name": "Esguerra M." }, { "name": "Mamyrbekov A." }, { "name": "Munk C." }, { "name": "Keseru G.M." }, { "name": "Gloriam D.E." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkx1109", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "2018 GPCRdb publication", "metadata": { "title": "GPCRdb in 2018: Adding GPCR structure models and ligands", "abstract": "© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.G protein-coupled receptors are the most abundant mediators of both human signalling processes and therapeutic effects. Herein, we report GPCRome-wide homology models of unprecedented quality, and roughly 150 000 GPCR ligands with data on biological activities and commercial availability. Based on the strategy of 'Less model - more Xtal', each model exploits both a main template and alternative local templates. This achieved higher similarity to new structures than any of the existing resources, and refined crystal structures with missing or distorted regions. Models are provided for inactive, intermediate and active states - except for classes C and F that so far only have inactive templates. The ligand database has separate browsers for: (i) target selection by receptor, family or class, (ii) ligand filtering based on cross-experiment activities (min, max and mean) or chemical properties, (iii) ligand source data and (iv) commercial availability. SMILES structures and activity spreadsheets can be downloaded for further processing. Furthermore, three recent landmark publications on GPCR drugs, G protein selectivity and genetic variants have been accompanied with resources that now let readers view and analyse the findings themselves in GPCRdb. Altogether, this update will enable scientific investigation for the wider GPCR community. GPCRdb is available at http://www.gpcrdb.org.", "date": "2018-01-01T00:00:00Z", "citationCount": 299, "authors": [ { "name": "Pandy-Szekeres G." }, { "name": "Munk C." }, { "name": "Tsonkov T.M." }, { "name": "Mordalski S." }, { "name": "Harpsoe K." }, { "name": "Hauser A.S." }, { "name": "Bojarski A.J." }, { "name": "Gloriam D.E." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1038/s41586-020-2888-2", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "GPCR isoform resource as available in the GPCRdb", "metadata": { "title": "Combinatorial expression of GPCR isoforms affects signalling and drug responses", "abstract": "© 2020, The Author(s), under exclusive licence to Springer Nature Limited.G-protein-coupled receptors (GPCRs) are membrane proteins that modulate physiology across human tissues in response to extracellular signals. GPCR-mediated signalling can differ because of changes in the sequence1,2 or expression3 of the receptors, leading to signalling bias when comparing diverse physiological systems4. An underexplored source of such bias is the generation of functionally diverse GPCR isoforms with different patterns of expression across different tissues. Here we integrate data from human tissue-level transcriptomes, GPCR sequences and structures, proteomics, single-cell transcriptomics, population-wide genetic association studies and pharmacological experiments. We show how a single GPCR gene can diversify into several isoforms with distinct signalling properties, and how unique isoform combinations expressed in different tissues can generate distinct signalling states. Depending on their structural changes and expression patterns, some of the detected isoforms may influence cellular responses to drugs and represent new targets for developing drugs with improved tissue selectivity. Our findings highlight the need to move from a canonical to a context-specific view of GPCR signalling that considers how combinatorial expression of isoforms in a particular cell type, tissue or organism collectively influences receptor signalling and drug responses.", "date": "2020-11-26T00:00:00Z", "citationCount": 39, "authors": [ { "name": "Marti-Solano M." }, { "name": "Crilly S.E." }, { "name": "Malinverni D." }, { "name": "Munk C." }, { "name": "Harris M." }, { "name": "Pearce A." }, { "name": "Quon T." }, { "name": "Mackenzie A.E." }, { "name": "Wang X." }, { "name": "Peng J." }, { "name": "Tobin A.B." }, { "name": "Ladds G." }, { "name": "Milligan G." }, { "name": "Gloriam D.E." }, { "name": "Puthenveedu M.A." }, { "name": "Babu M.M." } ], "journal": "Nature" } }, { "doi": "10.1038/s41592-018-0302-x", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "GPCR construct design tool as available in the GPCRdb", "metadata": { "title": "An online resource for GPCR structure determination and analysis", "abstract": "© 2019, Springer Nature America, Inc.G-protein-coupled receptors (GPCRs) transduce physiological and sensory stimuli into appropriate cellular responses and mediate the actions of one-third of drugs. GPCR structural studies have revealed the general bases of receptor activation, signaling, drug action and allosteric modulation, but so far cover only 13% of nonolfactory receptors. We broadly surveyed the receptor modifications/engineering and methods used to produce all available GPCR crystal and cryo-electron microscopy (cryo-EM) structures, and present an interactive resource integrated in GPCRdb (http://www.gpcrdb.org) to assist users in designing constructs and browsing appropriate experimental conditions for structure studies.", "date": "2019-02-01T00:00:00Z", "citationCount": 85, "authors": [ { "name": "Munk C." }, { "name": "Mutt E." }, { "name": "Isberg V." }, { "name": "Nikolajsen L.F." }, { "name": "Bibbe J.M." }, { "name": "Flock T." }, { "name": "Hanson M.A." }, { "name": "Stevens R.C." }, { "name": "Deupi X." }, { "name": "Gloriam D.E." } ], "journal": "Nature Methods" } }, { "doi": "10.1093/nar/gkac1013", "pmid": "36395823", "pmcid": null, "type": [ "Primary" ], "version": null, "note": "2023 GPCRdb publication", "metadata": null }, { "doi": "10.1038/s41594-021-00675-6", "pmid": "34759374", "pmcid": null, "type": [], "version": null, "note": "An online GPCR structure analysis platform", "metadata": { "title": "An online GPCR structure analysis platform", "abstract": "© 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.We present an online, interactive platform for comparative analysis of all available G-protein coupled receptor (GPCR) structures while correlating to functional data. The comprehensive platform encompasses structure similarity, secondary structure, protein backbone packing and movement, residue–residue contact networks, amino acid properties and prospective design of experimental mutagenesis studies. This lets any researcher tap the potential of sophisticated structural analyses enabling a plethora of basic and applied receptor research studies.", "date": "2021-11-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Kooistra A.J." }, { "name": "Munk C." }, { "name": "Hauser A.S." }, { "name": "Gloriam D.E." } ], "journal": "Nature Structural and Molecular Biology" } } ], "credit": [ { "name": "GPCRDB", "email": "info@gpcr.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Provider" ], "note": "Contact for general and support questions regarding the GPCRdb" }, { "name": "David Gloriam", "email": null, "url": "https://drug.ku.dk/staff/?pure=en/persons/352279", "orcidid": "https://orcid.org/0000-0002-4299-7561", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Head of the GPCRdb" } ], "community": null, "owner": "GPCRDB", "additionDate": "2015-02-04T09:25:19Z", "lastUpdate": "2024-02-14T13:13:19.740941Z", "editPermission": { "type": "group", "authors": [ "AJK_dev", "mbermudez1" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HMMER hmmscan (EBI)", "description": "HMMER3 hmmscan is used to search sequences against collections of profiles.", "homepage": "https://www.ebi.ac.uk/jdispatcher/pfa/hmmer3_hmmscan", "biotoolsID": "hmmer_hmmscan_ebi", "biotoolsCURIE": "biotools:hmmer_hmmscan_ebi", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "hmmer3", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1364", "term": "Hidden Markov model" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2066", "term": "Database hits (sequence) format" } ] }, { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [ "EBI Tools", "Job Dispatcher Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "http://hmmer.org/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.ebi.ac.uk/jdispatcher/help", "type": [ "General" ], "note": null }, { "url": "http://hmmer.org/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkr367", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "HMMER web server: Interactive sequence similarity searching", "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).", "date": "2011-07-01T00:00:00Z", "citationCount": 3538, "authors": [ { "name": "Finn R.D." }, { "name": "Clements J." }, { "name": "Eddy S.R." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "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.", "date": "2022-07-05T00:00:00Z", "citationCount": 699, "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." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Sean Eddy", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Job Dispatcher", "email": null, "url": "https://www.ebi.ac.uk/jdispatcher", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "jdispatcher", "additionDate": "2022-11-03T15:52:41.693905Z", "lastUpdate": "2024-02-08T10:58:38.007948Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HMMER phmmer (EBI)", "description": "HMMER3 phmmer is used to search one or more sequences against a sequence database.", "homepage": "https://www.ebi.ac.uk/jdispatcher/pfa/hmmer3_phmmer", "biotoolsID": "hmmer_phmmer_ebi", "biotoolsCURIE": "biotools:hmmer_phmmer_ebi", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "hmmer3", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1364", "term": "Hidden Markov model" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2066", "term": "Database hits (sequence) format" } ] }, { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [ "EBI Tools", "Job Dispatcher Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "http://hmmer.org/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.ebi.ac.uk/jdispatcher/help", "type": [ "General" ], "note": null }, { "url": "http://hmmer.org/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkr367", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "HMMER web server: Interactive sequence similarity searching", "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).", "date": "2011-07-01T00:00:00Z", "citationCount": 3538, "authors": [ { "name": "Finn R.D." }, { "name": "Clements J." }, { "name": "Eddy S.R." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "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.", "date": "2022-07-05T00:00:00Z", "citationCount": 699, "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." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Sean Eddy", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Job Dispatcher", "email": null, "url": "https://www.ebi.ac.uk/jdispatcher", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "jdispatcher", "additionDate": "2022-11-03T15:52:37.739953Z", "lastUpdate": "2024-02-08T10:54:28.651795Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }