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{ "count": 222, "next": "?page=2", "previous": null, "list": [ { "name": "BioSurfDB", "description": "BioSurfDB is a online database for biodegradation and biosurfactants.", "homepage": "https://www.biosurfdb.org", "biotoolsID": "biosurfdb", "biotoolsCURIE": "biotools:biosurfdb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1385", "term": "Hybrid sequence alignment" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0349", "term": "Sequence database search (by property)" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_1026", "term": "Gene symbol" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1027", "term": "Gene ID (NCBI)" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2299", "term": "Gene name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3297", "term": "Biotechnology" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_0821", "term": "Enzymes" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/database/bav033", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "BioSurfDB: Knowledge and algorithms to support biosurfactants and biodegradation studies", "abstract": "Crude oil extraction, transportation and use provoke the contamination of countless ecosystems. Therefore, bioremediation through surfactants mobilization or biodegradation is an important subject, both economically and environmentally. Bioremediation research had a great boost with the recent advances in Metagenomics, as it enabled the sequencing of uncultured microorganisms providing new insights on surfactant-producing and/or oil-degrading bacteria. Many research studies are making available genomic data from unknown organisms obtained from metagenomics analysis of oil-contaminated environmental samples. These new datasets are presently demanding the development of new tools and data repositories tailored for the biological analysis in a context of bioremediation data analysis. This work presents BioSurfDB, www.biosurfdb.org, a curated relational information system integrating data from: (i) metagenomes; (ii) organisms; (iii) biodegradation relevant genes; proteins and their metabolic pathways; (iv) bioremediation experiments results, with specific pollutants treatment efficiencies by surfactant producing organisms; and (v) a biosurfactant-curated list, grouped by producing organism, surfactant name, class and reference. The main goal of this repository is to gather information on the characterization of biological compounds and mechanisms involved in biosurfactant production and/or biodegradation and make it available in a curated way and associated with a number of computational tools to support studies of genomic and metagenomic data.", "date": "2015-01-01T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Oliveira J.S." }, { "name": "Araujo W." }, { "name": "Sales A.I.L." }, { "name": "De Brito Guerra A." }, { "name": "Da Silva Araujo S.C." }, { "name": "De Vasconcelos A.T.R." }, { "name": "Agnez-Lima L.F." }, { "name": "Freitas A.T." } ], "journal": "Database" } } ], "credit": [ { "name": "Jorge S. Oliveira", "email": "jorge.oliveira@tecnico.ulisboa.pt", "url": "https://web.tecnico.ulisboa.pt/jorge.oliveira/", "orcidid": "https://orcid.org/0000-0001-6425-2176", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ana Teresa Freitas", "email": "ana.freitas@tecnico.ulisboa.pt", "url": null, "orcidid": "http://orcid.org/0000-0003-4638-2879", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ana Tereza Ribeiro de Vasconcelos", "email": "atrv@lncc.br", "url": null, "orcidid": "http://orcid.org/0000-0002-4632-2086", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Lucymara Fassarella Agnez-Lima", "email": "lucymara.agnez@ufrn.br", "url": null, "orcidid": "http://orcid.org/0000-0003-0642-3162", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Gil Poiares-Oliveira", "email": "gpo@biodata.pt", "url": "https://web.tecnico.ulisboa.pt/gil.oliveira", "orcidid": "https://orcid.org/0000-0003-4638-2879", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null } ], "owner": "ELIXIR-PT", "additionDate": "2025-04-29T17:07:56.642694Z", "lastUpdate": "2025-04-29T17:35:41.655075Z", "editPermission": { "type": "group", "authors": [ "gpo" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "samclip", "description": "Filter SAM file for soft and hard clipped alignments", "homepage": "https://github.com/tseemann/samclip", "biotoolsID": "samclip", "biotoolsCURIE": "biotools:samclip", "version": [ "0.4.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/tseemann/samclip", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://anaconda.org/bioconda/samclip", "type": "Software package", "note": null, "version": "0.4.0" } ], "documentation": [ { "url": "https://github.com/tseemann/samclip", "type": [ "General" ], "note": null } ], "publication": [], "credit": [], "owner": "emmcauley", "additionDate": "2025-04-21T21:06:51.624399Z", "lastUpdate": "2025-04-21T21:06:51.626575Z", "editPermission": { "type": "group", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SILVA rRNA database", "description": "SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukaryota).", "homepage": "http://www.arb-silva.de", "biotoolsID": "silva", "biotoolsCURIE": "biotools:silva", "version": [], "otherID": [ { "value": "RRID:SCR_006423", "type": "rrid", "version": null } ], "relation": [ { "biotoolsID": "silvangs", "type": "usedBy" }, { "biotoolsID": "d3hub", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1097", "term": "Sequence accession (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_1868", "term": "Taxon" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_1046", "term": "Strain name" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_1088", "term": "Article ID" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] }, { "data": { "uri": "http://edamontology.org/data_2909", "term": "Organism name" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] } ], "note": "The search and retrieval functions of the SILVA website can be used to build custom subsets of sequences. In addition to simple searches e.g. for accession numbers, organism names, taxonomic entities, or publication DOI/PubMed IDs, complex queries over several database fields using constraints such as sequence length or quality values are possible. The results can be sorted according to accession numbers, organism names, sequence length, sequence and alignment quality and Pintail values. The search results show accession number, organism name, sequence length, sequence quality values, taxonomic classifications, and links to view the full sequence record on SILVA and on ENA. Sequences found via search and added to download cart can be downloaded as FASTA and ARB files.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] } ], "note": "SILVA Incremental Aligner (SINA) is used to align the rRNA gene databases provided by SILVA, as well as user submitted sequences. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. Aligned sequences can be dowloaded as FASTA or ARB files", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3460", "term": "Taxonomic classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Sequence alignment (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] }, { "data": { "uri": "http://edamontology.org/data_1872", "term": "Taxonomic classification" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "SINA can also operate as a taxonomic classification tool. It uses the search result to derive a classification with the LCA (lowest common ancestor) method. Each query sequence is assigned the shared part of the classifications of the search results. Aligned sequences can be dowloaded as FASTA or ARB files Taxonomic classification results can be downloaded as csv files.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2419", "term": "Primer and probe design" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1207", "term": "nucleotide" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "The SILVA Probe Match and Evaluation Tool detects and displays all occurrences of a given probe or primer sequence in the SILVA datasets. TestPrime allows you to evaluate the performance of primer pairs by running an in silico PCR on the SILVA databases. From the results of the PCR, TestPrime computes coverages for each taxonomic group in all of the taxonomies offered by SILVA.", "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" }, { "uri": "http://edamontology.org/topic_3050", "term": "Biodiversity" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_0632", "term": "Probes and primers" } ], "operatingSystem": [], "language": [], "license": "CC-BY-4.0", "collectionID": [ "de.NBI", "de.NBI-biodata", "DSMZ Digital Diversity" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://www.arb-silva.de/browser/", "type": [ "Service" ], "note": "SILVA Taxonomy Browser" }, { "url": "https://www.arb-silva.de/search/", "type": [ "Service" ], "note": "SILVA metadata search" }, { "url": "https://www.arb-silva.de/aligner/", "type": [ "Service" ], "note": "ACT: Alignment, Classification and Tree Service" }, { "url": "https://www.arb-silva.de/search/testprobe/", "type": [ "Service" ], "note": "SILVA Probe Match and Evaluation Tool" }, { "url": "https://www.arb-silva.de/search/testprime/", "type": [ "Service" ], "note": "SILVA Primer Evaluation Tool" }, { "url": "https://treeviewer.arb-silva.de/", "type": [ "Service" ], "note": "Web-based viewer for the SILVA guide trees" } ], "download": [ { "url": "https://www.arb-silva.de/download/archive/", "type": "Downloads page", "note": "SILVA dataset archive", "version": null } ], "documentation": [ { "url": "https://www.arb-silva.de/silva-license-information/", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.arb-silva.de/contact/", "type": [ "Citation instructions" ], "note": null }, { "url": "http://www.arb-silva.de/documentation/", "type": [ "General" ], "note": null }, { "url": "https://www.arb-silva.de/documentation/faqs/", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gks1219", "pmid": "23193283", "pmcid": "PMC3531112", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools", "abstract": "SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3194 778 small subunit and 288717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches. © The Author(s) 2012.", "date": "2013-01-01T00:00:00Z", "citationCount": 20831, "authors": [ { "name": "Quast C." }, { "name": "Pruesse E." }, { "name": "Yilmaz P." }, { "name": "Gerken J." }, { "name": "Schweer T." }, { "name": "Yarza P." }, { "name": "Peplies J." }, { "name": "Glockner F.O." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkt1209", "pmid": "24293649", "pmcid": "PMC3965112", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The SILVA and \"all-species Living Tree Project (LTP)\" taxonomic frameworks", "abstract": "SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources. © 2013 The Author(s). Published by Oxford University Press.", "date": "2014-01-01T00:00:00Z", "citationCount": 2372, "authors": [ { "name": "Yilmaz P." }, { "name": "Parfrey L.W." }, { "name": "Yarza P." }, { "name": "Gerken J." }, { "name": "Pruesse E." }, { "name": "Quast C." }, { "name": "Schweer T." }, { "name": "Peplies J." }, { "name": "Ludwig W." }, { "name": "Glockner F.O." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkm864", "pmid": "17947321", "pmcid": "PMC2175337", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB", "abstract": "Sequencing ribosomal RNA (rRNA) genes is currently the method of choice for phylogenetic reconstruction, nucleic acid based detection and quantification of microbial diversity. The ARB software suite with its corresponding rRNA datasets has been accepted by researchers worldwide as a standard tool for large scale rRNA analysis. However, the rapid increase of publicly available rRNA sequence data has recently hampered the maintenance of comprehensive and curated rRNA knowledge databases. A new system, SILVA (from Latin silva, forest), was implemented to provide a central comprehensive web resource for up to date, quality controlled databases of aligned rRNA sequences from the Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies, carry a rich set of sequence associated contextual information, have multiple taxonomic classifications, and the latest validly described nomenclature. Furthermore, two precompiled sequence datasets compatible with ARB are offered for download on the SILVA website: (i) the reference (Ref) datasets, comprising only high quality, nearly full length sequences suitable for in-depth phylogenetic analysis and probe design and (ii) the comprehensive Parc datasets with all publicly available rRNA sequences longer than 300 nucleotides suitable for biodiversity analyses. The latest publicly available database release 91 (August 2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689 large subunit rRNAs. © 2007 The Author(s).", "date": "2007-12-01T00:00:00Z", "citationCount": 5145, "authors": [ { "name": "Pruesse E." }, { "name": "Quast C." }, { "name": "Knittel K." }, { "name": "Fuchs B.M." }, { "name": "Ludwig W." }, { "name": "Peplies J." }, { "name": "Glockner F.O." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/bioinformatics/bts252", "pmid": "22556368", "pmcid": "PMC3389763", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes", "abstract": "Motivation: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements.Results: In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. © The Author(s) 2012. Published by Oxford University Press.", "date": "2012-07-01T00:00:00Z", "citationCount": 2352, "authors": [ { "name": "Pruesse E." }, { "name": "Peplies J." }, { "name": "Glockner F.O." } ], "journal": "Bioinformatics" } }, { "doi": "10.1016/j.jbiotec.2017.06.1198", "pmid": "28648396", "pmcid": null, "type": [ "Review" ], "version": null, "note": null, "metadata": { "title": "25 years of serving the community with ribosomal RNA gene reference databases and tools", "abstract": "SILVA (lat. forest) is a comprehensive web resource, providing services around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich started the integrated software workbench ARB (lat. tree) to support high-quality phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes. At that time, the ARB project maintained both, the sequence reference datasets and the software package for data analysis. In 2005, with the massive increase of DNA sequence data, the maintenance of the software system ARB and the corresponding rRNA databases SILVA was split between Munich and the Microbial Genomics and Bioinformatics Research Group in Bremen. ARB has been continuously developed to include new features and improve the usability of the workbench. Thousands of users worldwide appreciate the seamless integration of common analysis tools under a central graphical user interface, in combination with its versatility. The first SILVA release was deployed in February 2007 based on the EMBL-EBI/ENA release 89. Since then, full SILVA releases offering the database content in various flavours are published at least annually, complemented by intermediate web-releases where only the SILVA web dataset is updated. SILVA is the only rDNA database project worldwide where special emphasis is given to the consistent naming of clades of uncultivated (environmental) sequences, where no validly described cultivated representatives are available. Also exclusive for SILVA is the maintenance of both comprehensive aligned 16S/18S rDNA and 23S/28S rDNA sequence datasets. Furthermore, the SILVA alignments and trees were designed to include Eukaryota, another unique feature among rDNA databases. With the termination of the European Ribosomal RNA Database Project in 2007, the SILVA database has become the authoritative rDNA database project for Europe. The application spectrum of ARB and SILVA ranges from biodiversity analysis, medical diagnostics, to biotechnology and quality control for academia and industry.", "date": "2017-11-10T00:00:00Z", "citationCount": 578, "authors": [ { "name": "Glockner F.O." }, { "name": "Yilmaz P." }, { "name": "Quast C." }, { "name": "Gerken J." }, { "name": "Beccati A." }, { "name": "Ciuprina A." }, { "name": "Bruns G." }, { "name": "Yarza P." }, { "name": "Peplies J." }, { "name": "Westram R." }, { "name": "Ludwig W." } ], "journal": "Journal of Biotechnology" } }, { "doi": "10.1186/s12859-017-1841-3", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "SILVA tree viewer: Interactive web browsing of the SILVA phylogenetic guide trees", "abstract": "Background: Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. Results: The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA Tree Viewer is based on Web Geographic Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer enables access to two phylogenetic (guide) trees provided by the SILVA database: the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences, clustered at 99% sequence identity and the LSU Ref inferred from high-quality, full-length large subunit sequences. Conclusions: The Tree Viewer provides tree navigation, search and browse tools as well as an interactive feedback system to collect any kinds of requests ranging from taxonomy to data curation and improving the tool itself.", "date": "2017-09-30T00:00:00Z", "citationCount": 28, "authors": [ { "name": "Beccati A." }, { "name": "Gerken J." }, { "name": "Quast C." }, { "name": "Yilmaz P." }, { "name": "Glockner F.O." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures", "email": "hub@dsmz.de", "url": "https://www.dsmz.de", "orcidid": null, "gridid": "grid.420081.f", "rorid": "02tyer376", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "contact@arb-silva.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "silva", "additionDate": "2016-09-30T15:59:05Z", "lastUpdate": "2025-01-22T09:59:03.064970Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "TREND Protein Evolution Function", "description": "TREND is a platform that allows researchers to explore protein function and evolution identifying protein features, gene neighborhoods and operons, clustering neighboring genes, and integrating all these data into phylogenomic context and cross-referencing with RefSeq, Pfam, CDD and MiST databases. The platform provides ample opportunities for adjusting each step of the analysis.", "homepage": "http://trend.evobionet.com/", "biotoolsID": "trend_protein_evolution_function", "biotoolsCURIE": "biotools:trend_protein_evolution_function", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" }, { "uri": "http://edamontology.org/operation_0323", "term": "Phylogenetic inference" }, { "uri": "http://edamontology.org/operation_0291", "term": "Sequence clustering" }, { "uri": "http://edamontology.org/operation_2995", "term": "Sequence classification" }, { "uri": "http://edamontology.org/operation_0246", "term": "Protein domain recognition" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1384", "term": "Protein sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1233", "term": "Sequence set (protein)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [ { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] }, { "data": { "uri": "http://edamontology.org/data_1900", "term": "NCBI locus tag" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2385", "term": "RefSeq accession (protein)" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1384", "term": "Protein sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [ { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] }, { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] }, { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_1245", "term": "Sequence cluster (protein)" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_3299", "term": "Evolutionary biology" }, { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" }, { "uri": "http://edamontology.org/topic_0194", "term": "Phylogenomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://trend.evobionet.com/help", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkaa243", "pmid": "32282909", "pmcid": "PMC7319448", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "TREND: a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses", "abstract": "Key steps in a computational study of protein function involve analysis of (i) relationships between homologous proteins, (ii) protein domain architecture and (iii) gene neighborhoods the corresponding proteins are encoded in. Each of these steps requires a separate computational task and sets of tools. Currently in order to relate protein features and gene neighborhoods information to phylogeny, researchers need to prepare all the necessary data and combine them by hand, which is time-consuming and error-prone. Here, we present a new platform, TREND (tree-based exploration of neighborhoods and domains), which can perform all the necessary steps in automated fashion and put the derived information into phylogenomic context, thus making evolutionary based protein function analysis more efficient. A rich set of adjustable components allows a user to run the computational steps specific to his task. TREND is freely available at http://trend.zhulinlab.org.", "date": "2021-01-01T00:00:00Z", "citationCount": 33, "authors": [ { "name": "Gumerov V.M." }, { "name": "Zhulin I.B." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkac034", "pmid": "35100406", "pmcid": "PMC8860576", "type": [ "Other" ], "version": null, "note": "Can be also accessed at this URL: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac034/6517937", "metadata": { "title": "Erratum: TREND: A platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses (Nucleic Acids Research DOI: 10.1093/nar/gkaa243)", "abstract": "TheURL address of the web server published in this article has been changed fromhttp://trend.zhulinlab.org to http://trend. evobionet.com/.", "date": "2022-02-22T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Gumerov V.M." }, { "name": "Zhulin I.B." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Vadim Gumerov", "email": "gumerov.1@osu.edu", "url": null, "orcidid": "https://orcid.org/0000-0003-1670-7679", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "vadim", "additionDate": "2020-11-09T21:38:53Z", "lastUpdate": "2024-12-17T20:42:49.942166Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Jalview", "description": "Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. 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"http://edamontology.org/format_3311", "term": "RNAML" }, { "uri": "http://edamontology.org/format_1947", "term": "GCG MSF" }, { "uri": "http://edamontology.org/format_3015", "term": "Pileup" }, { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_1915", "term": "Format" } ] }, { "data": { "uri": "http://edamontology.org/data_0886", "term": "Structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1961", "term": "Stockholm format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": 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(.jvp);\nJalview Feature File (.features, .jvfeatures);\nJalview Annotations File (.annotations, .jvannotations);\nPredicted Aligned Error (PAE) Matrix File (.json)\n...\nOther Output formats:\nPFAM (.pfam);\nBioJS (.biojs) (interactive HTML/Javascript);\nJalview Project File (.jvp);", "cmd": null } ], "toolType": [ "Desktop application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-3.0", "collectionID": [ "ELIXIR-UK" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "UK" ], "elixirCommunity": [], "link": [ { "url": "https://discourse.jalview.org/", "type": [ "Discussion forum" ], "note": null }, { "url": "https://issues.jalview.org/", "type": [ "Issue tracker" ], "note": null }, { "url": "https://www.jalview.org/development/jalview_develop/", "type": [ "Other" ], "note": "Latest development version" }, { "url": "https://source.jalview.org/crucible/browse/jalview", "type": [ "Repository" ], "note": null }, { "url": "https://twitter.com/Jalview", "type": [ "Social media" ], "note": "Twitter feed" }, { "url": "https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw", "type": [ "Social media" ], "note": "YouTube training videos" } ], "download": [ { "url": "https://www.jalview.org/download", "type": "Downloads page", "note": null, "version": null }, { "url": "https://www.jalview.org/download/source/", "type": "Source code", "note": null, "version": null }, { "url": "https://www.jalview.org/download/?os=all", "type": "Binaries", "note": "Binaries for all platforms", "version": null }, { "url": "https://www.jalview.org/favicon.svg", "type": "Icon", "note": null, "version": null }, { "url": "https://www.jalview.org/download/other/jar/", "type": "Binaries", "note": "Executable JAR file", "version": null } ], "documentation": [ { "url": "https://www.jalview.org/about/citation", "type": [ "Citation instructions" ], "note": null }, { "url": "https://www.jalview.org/training/", "type": [ "Training material" ], "note": "Hands-on exercises, Training courses and Training videos" }, { "url": "https://www.jalview.org/help/faq", "type": [ "FAQ" ], "note": null }, { "url": "https://www.jalview.org/help/documentation/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp033", "pmid": "19151095", "pmcid": "PMC2672624", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Jim Procter", "email": null, "url": "http://www.lifesci.dundee.ac.uk/people/jim-procter", "orcidid": "https://orcid.org/0000-0002-7865-7382", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Geoff Barton", "email": null, "url": "https://www.lifesci.dundee.ac.uk/people/geoff-barton", "orcidid": "https://orcid.org/0000-0002-9014-5355", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "ben_s", "additionDate": "2019-02-13T17:01:40Z", "lastUpdate": "2024-11-28T10:07:42.658684Z", "editPermission": { "type": "group", "authors": [ "ben_s", "jimprocter" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "msa", "description": "Display multiple-sequence alignment. The tool is also available as R/BioConductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms.", "homepage": "http://msa.biojs.net", "biotoolsID": "msa", "biotoolsCURIE": "biotools:msa", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] }, { "data": { "uri": "http://edamontology.org/data_1711", "term": "Sequence alignment image" }, "format": [ { "uri": "http://edamontology.org/format_3547", "term": "Image format" } ] }, { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_2305", "term": "GFF" } ] } ], "note": "Visualizes multiple sequence alignment, calculates conservation, shows sequence logo, applies multiple color schemes A multiple sequence alignment (ClustalW, FASTA, ...) Exports selected sequences and regions from the alignment Images are exported in PNG Export sequences in FASTA format Export features in GFF\nNOTE: Actually, all these output types of data should instead be under separate \"constant\" operations, while the visualisation should be an unary operation, perhaps without an output.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1948", "term": "nbrf/pir" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_1935", "term": "GCG" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_1927", "term": "EMBL format" }, { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" } ] }, 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tool", "Library" ], "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_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript" ], "license": "Apache-2.0", "collectionID": [ "Rostlab tools", "Bioconductor", "BioJS" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/wilzbach/msa", "type": [ "Repository" ], "note": null }, { "url": "http://biojs.io/", "type": [ "Software catalogue" ], "note": null }, { "url": "http://github.com/wilzbach/msa", "type": [ "Helpdesk" ], "note": null }, { "url": "http://www.bioinf.jku.at/software/msa/", "type": [ "Mirror" ], "note": null } 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The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.", "date": "2015-01-01T00:00:00Z", "citationCount": 2315, "authors": [ { "name": "Huber W." }, { "name": "Carey V.J." }, { "name": "Gentleman R." }, { "name": "Anders S." }, { "name": "Carlson M." }, { "name": "Carvalho B.S." }, { "name": "Bravo H.C." }, { "name": "Davis S." }, { "name": "Gatto L." }, { "name": "Girke T." }, { "name": "Gottardo R." }, { "name": "Hahne F." }, { "name": "Hansen K.D." }, { "name": "Irizarry R.A." }, { "name": "Lawrence M." }, { "name": "Love M.I." }, { "name": "MaCdonald J." }, { "name": "Obenchain V." }, { "name": "Oles A.K." }, { "name": "Pages H." }, { "name": "Reyes A." }, { "name": "Shannon P." }, { "name": "Smyth G.K." }, { "name": "Tenenbaum D." }, { "name": "Waldron L." }, { "name": "Morgan M." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "H. Pagès", "email": "hpages@fredhutch.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T14:57:29Z", "lastUpdate": "2024-11-25T14:35:14.288041Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Phymyco-DB", "description": "A database designed to help the mycologist community to access to fungal DNA markers data for phylogenetic analyses.", "homepage": "http://phymycodb.genouest.org/", "biotoolsID": "phymyco-db", "biotoolsCURIE": "biotools:phymyco-db", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Sequence alignment", "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://phymycodb.genouest.org/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0043117", "pmid": "23028445", "pmcid": "PMC3441585", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution", "abstract": "Background: In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept. Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation. Methods and Principal Findings: To facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ~20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples. Conclusion: PHYMYCO-DB offers the tools necessary to: (i) extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii) extract already performed alignments, to act as 'reference alignments', (iii) launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available. The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org. © 2012 Mahé et al.", "date": "2012-09-13T00:00:00Z", "citationCount": 37, "authors": [ { "name": "Mahe S." }, { "name": "Duhamel M." }, { "name": "Le Calvez T." }, { "name": "Guillot L." }, { "name": "Sarbu L." }, { "name": "Bretaudeau A." }, { "name": "Collin O." }, { "name": "Dufresne A." }, { "name": "Kiers E.T." }, { "name": "Vandenkoornhuyse P." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "GenOuest", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "GenOuest", "email": "support@genouest.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "GenOuest", "additionDate": "2015-01-21T15:12:26Z", "lastUpdate": "2024-11-25T14:25:53.229148Z", "editPermission": { "type": "group", "authors": [ "olivier.collin@irisa.fr" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Ensembl Genomes Fungi sequence search", "description": "Searches Ensembl Fungi sequences using Exonerate.", "homepage": "http://fungi.ensembl.org/Multi/enasearch", "biotoolsID": "ensembl_genomes_fungi_sequence_search", "biotoolsCURIE": "biotools:ensembl_genomes_fungi_sequence_search", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Ensembl Tools", "Ensembl Genomes", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://fungi.ensembl.org/info/website/help/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkv1157", "pmid": "26687719", "pmcid": "PMC4702834", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Ensembl 2016", "abstract": "The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. 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It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. 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JABAWS:MSA provides services for five multiple sequence alignment (MSA) methods (Probcons, T-coffee, Muscle, Mafft and ClustalW), and is the system employed by the Jalview multiple sequence analysis workbench since version 2.6. A fully functional, easy to set up server is provided as a Virtual Appliance (VA), which can be run on most operating systems that support a virtualization environment such as VMware or Oracle VirtualBox. JABAWS is also distributed as a Web Application aRchive (WAR) and can be configured to run on a single computer and/or a cluster managed by Grid Engine, LSF or other queuing systems that support DRMAA. JABAWS:MSA provides clients full access to each application's parameters, allows administrators to specify named parameter preset combinations and execution limits for each application through simple configuration files. The JABAWS command-line client allows integration of JABAWS services into conventional scripts. © The Author(s) 2011. 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The method is broadly based on the popular progressive approach to multiple alignment but avoids the most serious pitfalls caused by the greedy nature of this algorithm. With T-Coffee we pre-process a data set of all pair-wise alignments between the sequences. This provides us with a library of alignment information that can be used to guide the progressive alignment. Intermediate alignments are then based not only on the sequences to be aligned next but also on how all of the sequences align with each other. This alignment information can be derived from heterogeneous sources such as a mixture of alignment programs and/or structure superposition. Here, we illustrate the power of the approach by using a combination of local and global pair-wise alignments to generate the library. The resulting alignments are significantly more reliable, as determined by comparison with a set of 141 test cases, than any of the popular alternatives that we tried. The improvement, especially clear with the more difficult test cases, is always visible, regardless of the phylogenetic spread of the sequences in the tests. (C) 2000 Academic Press.", "date": "2000-09-08T00:00:00Z", "citationCount": 5803, "authors": [ { "name": "Notredame C." }, { "name": "Higgins D.G." }, { "name": "Heringa J." } ], "journal": "Journal of Molecular Biology" } } ], "credit": [ { "name": "Cedric Notredame", "email": "cedric.notredame@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "BioCatalogue", "additionDate": "2015-08-03T09:36:09Z", "lastUpdate": "2024-11-25T14:17:49.139161Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Muscle WS (jabaws)", "description": "Multiple sequence algnment tool.", "homepage": "http://www.compbio.dundee.ac.uk/jabaws", "biotoolsID": "muscle_ws_jabaws", "biotoolsCURIE": "biotools:muscle_ws_jabaws", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [ "MUSCLE", "JABAWS" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.biocatalogue.org/services/3759", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.compbio.dundee.ac.uk/jabaws/man_about.html", "type": [ "User manual" ], "note": null }, { "url": "http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/compbio/ws/server/MuscleWS.html", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btr304", "pmid": "21593132", "pmcid": "PMC3129525", "type": [ "Review" ], "version": null, "note": null, "metadata": { "title": "Java bioinformatics analysis web services for multiple sequence alignment-JABAWS:MSA", "abstract": "Summary: JABAWS is a web services framework that simplifies the deployment of web services for bioinformatics. 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Briefly, the algorithm works by seeding alignments with maximal exact matches (MEMs) and then extending seeds with the affine-gap Smith-Waterman algorithm (SW). The BWA-MEM algorithm performs local alignment. It may produce multiple primary alignments for different part of a query sequence. This is a crucial feature for long sequences. However, some tools such as Picards markDuplicates does not work with split alignments. One may consider to use option -M to flag shorter split hits as secondary.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1332", "term": "FASTA search results format" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [] } ], "note": "Find the SA coordinates of the input reads. reference sequence query sequence", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3429", "term": "Generation" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] } ], "note": "Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen reference sequence query sequence", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3429", "term": "Generation" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] } ], "note": "Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly. reference sequence", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] } ], "note": "Align query sequences in the in.fq file reference sequence", "cmd": null } ], "toolType": [ "Command-line tool", "Workbench" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "C" ], "license": "MIT", "collectionID": [ "BWA" ], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/bwa_index.cwl", "type": "Tool wrapper (CWL)", "note": null, "version": null }, { "url": "https://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/bwa_mem.cwl", "type": "Tool wrapper (CWL)", "note": null, "version": null }, { "url": "https://docker-ui.genouest.org/app/#/container/bioconda/bwa", "type": "Container file", "note": null, "version": null }, { "url": "https://anaconda.org/bioconda/bwa", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "http://bio-bwa.sourceforge.net/bwa.shtml", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp324", "pmid": "19451168", "pmcid": "PMC2705234", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Fast and accurate short read alignment with Burrows-Wheeler transform", "abstract": "Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows-Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10-20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. © 2009 The Author(s).", "date": "2009-07-01T00:00:00Z", "citationCount": 33667, "authors": [ { "name": "Li H." }, { "name": "Durbin R." } ], "journal": "Bioinformatics" } }, { "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": 146, "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": [], "version": null, "note": null, "metadata": { "title": "Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics", "abstract": "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": 54, "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": 66, "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": [], "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": 71, "authors": [ { "name": "Otto C." }, { "name": "Stadler P.F." }, { "name": "Hoffmann S." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/bioinformatics/btp698", "pmid": "20080505", "pmcid": "PMC2828108", "type": [], "version": null, "note": null, "metadata": { "title": "Fast and accurate long-read alignment with Burrows-Wheeler transform", "abstract": "Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashingbased software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. Availability: http://bio-bwa.sourceforge.net. Contact: rd@sanger.ac.uk © The Author(s) 2010. Published by Oxford University Press.", "date": "2010-01-15T00:00:00Z", "citationCount": 8584, "authors": [ { "name": "Li H." }, { "name": "Durbin R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "bwa team", "email": "bio-bwa-help@sourceforge.net", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Heng Li", "email": "me@liheng.org", "url": "http://www.liheng.org/", "orcidid": "http://orcid.org/0000-0003-4874-2874", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "seqwiki_import", "additionDate": "2017-01-13T13:13:56Z", "lastUpdate": "2024-11-25T14:09:49.679089Z", "editPermission": { "type": "group", "authors": [ "swohlgemuth" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "IPK BLAST Server", "description": "A homology search against the current barley sequences resources is provided. The complete sequences data set comprises the whole genome shotgun assemblies of the cultivars Morex, Barke and Bowman as well as the high and low confidence gene sets. The newest POPSEQ anchoring data is integrated. Furthermore, the barley exome capture targets are provided. Additionally, resources like bacterial artificial chromosome assemblies, BAC end sequences and full length cDNAs are included.", "homepage": "http://webblast.ipk-gatersleben.de", "biotoolsID": "ipk_blast", "biotoolsCURIE": "biotools:ipk_blast", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "blast", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1921", "term": "Alignment format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" } ], "operatingSystem": [ "Linux" ], "language": [ "Java" ], "license": null, "collectionID": [ "denbi-gcbn", "de.NBI", "BLAST" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://dx.doi.org/10.3835/plantgenome2015.06.0038", "type": [ "Citation instructions" ], "note": null }, { "url": "http://webblast.ipk-gatersleben.de/barley_ibsc/docs/blast_databases.html", "type": [ "General" ], "note": null }, { "url": "http://webblast.ipk-gatersleben.de/ryeselect/docs/blast_databases.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.3835/plantgenome2015.06.0038", "pmid": "27898761", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "TransPLANT resources for triticeae genomic data", "abstract": "The genome sequences of many important Triticeae species, including bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT (http://www.transplantdb.eu) is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access.", "date": "2016-03-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Spannagl M." }, { "name": "Alaux M." }, { "name": "Lange M." }, { "name": "Bolser D.M." }, { "name": "Bader K.C." }, { "name": "Letellier T." }, { "name": "Kimmel E." }, { "name": "Flores R." }, { "name": "Pommier C." }, { "name": "Kerhornou A." }, { "name": "Walts B." }, { "name": "Nussbaumer T." }, { "name": "Grabmuller C." }, { "name": "Chen J." }, { "name": "Colmsee C." }, { "name": "Beier S." }, { "name": "Mascher M." }, { "name": "Schmutzer T." }, { "name": "Arend D." }, { "name": "Thanki A." }, { "name": "Ramirez-Gonzalez R." }, { "name": "Ayling M." }, { "name": "Ayling S." }, { "name": "Caccamo M." }, { "name": "Mayer K.F.X." }, { "name": "Scholz U." }, { "name": "Steinbach D." }, { "name": "Quesneville H." }, { "name": "Kersey P.J." } ], "journal": "Plant Genome" } } ], "credit": [ { "name": "Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ipk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Dr. Uwe Scholz", "email": "scholz@ipk-gatersleben.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Maintainer" ], "note": null }, { "name": "Dr. Uwe Scholz", "email": "scholz@ipk-gatersleben.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ipk", "additionDate": "2016-04-22T09:22:48Z", "lastUpdate": "2024-11-25T14:07:20.696381Z", "editPermission": { "type": "group", "authors": [ "ipk" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Ensembl Genomes Metazoa Blast", "description": "Searches Ensembl Metazoa sequences using Exonerate.", "homepage": "http://metazoa.ensembl.org/Multi/blastview", "biotoolsID": "ensembl_genomes_metazoa_blast", "biotoolsCURIE": "biotools:ensembl_genomes_metazoa_blast", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "blast", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "BLAST", "Ensembl Tools", "Ensembl Genomes", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://metazoa.ensembl.org/info/website/help/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkv1157", "pmid": "26687719", "pmcid": "PMC4702834", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Ensembl 2016", "abstract": "The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. 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This makes it possible to use the programs without having to download the code and get the programs to run. The results of all the programs are presented on a webpage and can easily be downloaded for further analysis. Additional measures are calculated for each program to make it easier to judge the individual predictions, and a consensus prediction taking all the programs into account is also calculated. This website is free and open to all users and there is no login requirement. 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Tools and databases are used in basic, veterinary and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. The IMGT/mAb-DB interface was developed for therapeutic antibodies and fusion proteins for immunological applications (FPIA). 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"confidence_flag": null }, { "name": "IMGT 3Dstructure-DB", "description": "IMGT/3Dstructure-DB is the IMGT® database for 3D structures of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins, related proteins of the immune system (RPI) and fusion proteins for immune applications (FPIA).\nAnnotation is based on the IMGT-ONTOLOGY concepts.", "homepage": "http://www.imgt.org/3Dstructure-DB/", "biotoolsID": "imgt_3dstructure", "biotoolsCURIE": "biotools:imgt_3dstructure", "version": [], "otherID": [], "relation": [ { "biotoolsID": "imgt", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/operation_0245", "term": "Protein structural motif recognition" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2858", "term": "Ontology concept" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1127", "term": "PDB ID" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2085", "term": "Structure report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "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_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3948", "term": "Immunoinformatics" }, { "uri": "http://edamontology.org/topic_0804", "term": "Immunology" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_3930", "term": "Immunogenetics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://www.imgt.org/download/3Dstructure-DB/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.imgt.org/3Dstructure-DB/doc/IMGT3DstructureDBHelp.shtml", "type": [ "User manual" ], "note": null }, { "url": "http://www.imgt.org/3Dstructure-DB/doc/progversion.html", "type": [ "Release notes" ], "note": "IMGT/3Dstructure-DB and IMGT/2Dstructure-DB program versions" }, { "url": "http://www.imgt.org/3Dstructure-DB/doc/datarelease.html", "type": [ "Release notes" ], "note": "http://www.imgt.org/3Dstructure-DB/doc/datarelease.html" } ], "publication": [ { "doi": "10.1093/nar/gkp946", "pmid": "19900967", "pmcid": "PMC2808948", "type": [], "version": null, "note": null, "metadata": { "title": "IMGT/3dstructure-DB and IMGT/domaingapalign: A database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MHcSF", "abstract": "IMGT/3Dstructure-DB is the three-dimensional (3D) structure database of IMGT. ®, the international ImMunoGenetics information system. ® that is acknowledged as the global reference in immunogenetics and immunoinformatics. IMGT/3Dstructure-DB contains 3D structures of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility complex (MHC) proteins, antigen receptor/antigen complexes (IG/Ag, TR/peptide/MHC) of vertebrates; 3D structures of related proteins of the immune system (RPI) of vertebrates and invertebrates, belonging to the immunoglobulin and MHC superfamilies (IgSF and MhcSF, respectively) and found in complexes with IG, TR or MHC. IMGT/3Dstructure-DB data are annotated according to the IMGT criteria, using IMGT/DomainGapAlign, and based on the IMGT-ONTOLOGY concepts and axioms. IMGT/3Dstructure-DB provides IMGT gene and allele identification (CLASSIFICATION), region and domain delimitations (DESCRIPTION), amino acid positions according to the IMGT unique numbering (NUMEROTATION) that are used in IMGT/3Dstructure-DB cards, results of contact analysis and renumbered flat files. In its Web version, the IMGT/DomainGapAlign tool analyses amino acid sequences, per domain. Coupled to the IMGT/Collier-de-Perles tool, it provides an invaluable help for antibody engineering and humanization design based on complementarity determining region (CDR) grafting as it precisely defines the standardized framework regions (FR-IMGT) and CDR-IMGT. IMGT/3Dstructure-DB and IMGT/DomainGapAlign are freely available at http://www.imgt.org. © The Author(s) 2009. Published by Oxford University Press.", "date": "2009-11-17T00:00:00Z", "citationCount": 207, "authors": [ { "name": "Ehrenmann F." }, { "name": "Kaas Q." }, { "name": "Lefranc M.-P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkh042", "pmid": "14681396", "pmcid": "PMC308776", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1101/pdb.prot5637", "pmid": "21632774", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Imgt/3Dstructure-DB: Querying the IMGT database for 3D structures in immunology and immunoinformatics (IG or antibodies, TR, MH, RPI, and FPIA)", "abstract": "", "date": "2011-06-01T00:00:00Z", "citationCount": 59, "authors": [ { "name": "Ehrenmann F." }, { "name": "Lefranc M.-P." } ], "journal": "Cold Spring Harbor Protocols" } }, { "doi": "10.1093/nar/gku1056", "pmid": "25378316", "pmcid": "PMC4383898", "type": [], "version": null, "note": null, "metadata": { "title": "IMGT R, the international ImMunoGeneTics information system R 25 years on", "abstract": "IMGT, the international ImMunoGeneTics information system (http://www.imgt.org) is the global reference in immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), IMGT marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) and proteins of the IgSF and MhSF superfamilies. IMGT is built on the IMGTONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and 3D structures. The concepts include the IMGTR standardized keywords (identification), IMGTR standardized labels (description), IMGTR standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGTR comprises 7 databases, 17 online tools and 15 000 pages of web resources, and provides a high-quality and integrated system for analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses, including NGS high-throughput data. Tools and databases are used in basic, veterinary and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. The IMGT/mAb-DB interface was developed for therapeutic antibodies and fusion proteins for immunological applications (FPIA). IMGTR is freely available at http://www.imgt.org.", "date": "2015-01-28T00:00:00Z", "citationCount": 402, "authors": [ { "name": "Lefranc M.-P." }, { "name": "Giudicelli V." }, { "name": "Duroux P." }, { "name": "Jabado-Michaloud J." }, { "name": "Folch G." }, { "name": "Aouinti S." }, { "name": "Carillon E." }, { "name": "Duvergey H." }, { "name": "Houles A." }, { "name": "Paysan-Lafosse T." }, { "name": "Hadi-Saljoqi S." }, { "name": "Sasorith S." }, { "name": "Lefranc G." }, { "name": "Kossida S." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Marie-Paule Lefranc", "email": "marie-paule.lefranc@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Patrice Duroux", "email": "patrice.duroux@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Sofia Kossida", "email": "sofia.kossida@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "vgiudicelli", "additionDate": "2017-04-22T18:19:37Z", "lastUpdate": "2024-11-25T14:00:15.256998Z", "editPermission": { "type": "group", "authors": [ "vgiudicelli", "skossida", "pduroux", "Joumana", "geraldine.folch" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "IMGT Allele-Align", "description": "IMGT/Allele-Align is the IMGT® tool for the comparison of two alleles highlighting the nucleotide and amino acid differences.", "homepage": "http://www.imgt.org/Allele-Align/", "biotoolsID": "IMGT_Allele-Align", "biotoolsCURIE": "biotools:IMGT_Allele-Align", "version": [], "otherID": [], "relation": [ { "biotoolsID": "imgt", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0804", "term": "Immunology" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": null, "pmid": "15089751", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "IMGT-ontology for immunogenetics and immunoinformatics", "abstract": "IMGT, the international ImMunoGeneTics information system® (http://imgt.cines.fr), is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrates, created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire LIGM. IMGT provides a common access to standardized data which include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, 2D and 3D structures. IMGT consists of several sequence databases (IMGT/LIGM-DB, IMGT/MHC-DB, IMGT/PRIMER-DB), one genome database (IMGT/GENE-DB) and one three-dimensional structure database (IMGT/3Dstructure-DB), interactive tools for sequence analysis (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/PhyloGene, IMGT/Allele-Align), for genome analysis (IMGT/GeneSearch, IMGT/GeneView, IMGT/LocusView) and for 3D structure analysis (IMGT/StructuralQuery), and Web resources (\"IMGT Marie-Paule page\") comprising 8000 HTML pages. IMGT other accesses include SRS, FTP, search by BLAST, etc. By its high quality and its easy data distribution, IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research, genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (scFv, phage displays, combinatorial libraries) and therapeutical approaches (grafts, immunotherapy). IMGT is freely available at http://imgt.cines.fr. © 2004 - IOS Press, Bioinformation Systems e.V. and the authors. All rights reserved.", "date": "2004-06-14T00:00:00Z", "citationCount": 91, "authors": [ { "name": "Lefranc M.-P." }, { "name": "Giudicelli V." }, { "name": "Ginestoux C." }, { "name": "Bosc N." }, { "name": "Folch G." }, { "name": "Guiraudou D." }, { "name": "Jabado-Michaloud J." }, { "name": "Magris S." }, { "name": "Scaviner D." }, { "name": "Thouvenin V." }, { "name": "Combres K." }, { "name": "Girod D." }, { "name": "Jeanjean S." }, { "name": "Protat C." }, { "name": "Monod M.Y." }, { "name": "Duprat E." }, { "name": "Kaas Q." }, { "name": "Pommie C." }, { "name": "Chaume D." }, { "name": "Lefranc G." } ], "journal": "In Silico Biology" } }, { "doi": null, "pmid": "15972004", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "IMGT-Choreography for immunogenetics and immunoinformatics", "abstract": "IMGT, the international ImMunoGeneTics information system® (http://imgt.cines.fr), was created in 1989 at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) which belong to the immunoglobulin superfamily (IgSF) and MHC superfamily (MhcSF). IMGT provides a common access to standardized data from genome, proteome, genetics and three-dimensional structures. The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY, a semantic specification of terms to be used in immunogenetics and immunoinformatics. IMGT-ONTOLOGY has been formalized using XML Schema (IMGT-ML) for interoperability with other information systems. We are developing Web services to automatically query IMGT databases and tools. This is the first step towards IMGT-Choreography which will trigger and coordinate dynamic interactions between IMGT Web services to process complex significant biological and clinical requests. IMGT-Choreography will further increase the IMGT leadership in immunogenetics and immunoinformatics for medical research (repertoire analysis of the IG antibody recognition sites and of the TR recognition sites in autoimmune and infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research (IG and TR repertoires in farm and wild life species), genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (single chain Fragment variable (scFv), phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (detection and follow-up of residual diseases) and therapeutical approaches (grafts, immunotherapy, vaccinology). IMGT is freely available at http://imgt.cines.fr. © 2005 IOS Press. All rights reserved.", "date": "2005-06-13T00:00:00Z", "citationCount": 74, "authors": [ { "name": "Lefranc M.-P." }, { "name": "Clement O." }, { "name": "Kaas Q." }, { "name": "Duprat E." }, { "name": "Chastellan P." }, { "name": "Coelho I." }, { "name": "Combres K." }, { "name": "Ginestoux C." }, { "name": "Giudicelli V." }, { "name": "Chaume D." }, { "name": "Lefranc G." } ], "journal": "In Silico Biology" } }, { "doi": "10.1093/nar/gku1056", "pmid": "25378316", "pmcid": "PMC4383898", "type": [], "version": null, "note": null, "metadata": { "title": "IMGT R, the international ImMunoGeneTics information system R 25 years on", "abstract": "IMGT, the international ImMunoGeneTics information system (http://www.imgt.org) is the global reference in immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), IMGT marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) and proteins of the IgSF and MhSF superfamilies. IMGT is built on the IMGTONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and 3D structures. The concepts include the IMGTR standardized keywords (identification), IMGTR standardized labels (description), IMGTR standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGTR comprises 7 databases, 17 online tools and 15 000 pages of web resources, and provides a high-quality and integrated system for analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses, including NGS high-throughput data. Tools and databases are used in basic, veterinary and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. The IMGT/mAb-DB interface was developed for therapeutic antibodies and fusion proteins for immunological applications (FPIA). IMGTR is freely available at http://www.imgt.org.", "date": "2015-01-28T00:00:00Z", "citationCount": 402, "authors": [ { "name": "Lefranc M.-P." }, { "name": "Giudicelli V." }, { "name": "Duroux P." }, { "name": "Jabado-Michaloud J." }, { "name": "Folch G." }, { "name": "Aouinti S." }, { "name": "Carillon E." }, { "name": "Duvergey H." }, { "name": "Houles A." }, { "name": "Paysan-Lafosse T." }, { "name": "Hadi-Saljoqi S." }, { "name": "Sasorith S." }, { "name": "Lefranc G." }, { "name": "Kossida S." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Patrice Duroux", "email": "patrice.duroux@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Joumana", "additionDate": "2019-12-20T10:37:20Z", "lastUpdate": "2024-11-25T13:59:59.697819Z", "editPermission": { "type": "group", "authors": [ "geraldine.folch", "vgiudicelli", "skossida", "pduroux", "Joumana" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "IMGT JunctionAnalysis", "description": "IMGT/JunctionAnalysis is the IMGT® tool for the analysis of the nucleotide sequences of the V-J and V-D-J junctions of the variable domains of the immunoglobulins (IG) or antibodies and T cell receptors (TR).\nAnalysis is based on the IMGT-ONTOLOGY concepts.", "homepage": "http://www.imgt.org/IMGT_jcta", "biotoolsID": "IMGT_JunctionAnalysis", "biotoolsCURIE": "biotools:IMGT_JunctionAnalysis", "version": [], "otherID": [], "relation": [ { "biotoolsID": "imgt", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0448", "term": "Sequence alignment analysis (conservation)" }, { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3948", "term": "Immunoinformatics" }, { "uri": "http://edamontology.org/topic_3930", "term": "Immunogenetics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.imgt.org/IMGT_jcta/user_guide", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bth945", "pmid": "15262823", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "IMGT/JunctionAnalysis: The first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs", "abstract": "Motivation: To create the enormous diversity of 1012 immunoglobulins (IG) and T cell receptors (TR) per individual, very complex mechanisms occur at the DNA level: the combinatorial diversity results from the junction of the variable (V), diversity (D) and joining (J) genes; the N-diversity represents the addition at random of nucleotides not encoded in the genome; and somatic hypermutations occur in IG rearranged sequences. The accurate annotation of the junction between V, D, J genes in rearranged IG and TR sequences represents therefore a huge challenge by its uniqueness and complexity. We developed IMGT/JunctionAnalysis to analyse automatically in detail the IG and TR junctions, according to the IMGT Scientific chart rules, based on the IMGT-ONTOLOGY concepts. Results: IMGT/JunctionAnalysis is the first tool forthe detailed analysis of the IG and TR complex V-J and V-D-J JUNCTION(s). It delimits, at the nucleotide level, the genes resulting from the combinatorial diversity. It identifies accurately the D genes in the junctions of IG heavy (IGH), TR beta (TRB) and delta (TRD) chains. It delimits the palindromic P-REGION(s) and the N-REGION(s) resulting from the N-diversity. It evaluates the number of somatic hypermutations for each gene, within the JUNCTION. IMGT/JunctionAnalysis is capable of analysing, in a single run, an unlimited number of junctions from the same species (currently human or mouse) and from the same locus. Availability: IMGT/JunctionAnalysis is available from the IMGT Home page at http://imgt.cines.fr. © Oxford University Press 2004; all rights reserved.", "date": "2004-01-01T00:00:00Z", "citationCount": 272, "authors": [ { "name": "Monod M.Y." }, { "name": "Giudicelli V." }, { "name": "Chaume D." }, { "name": "Lefranc M.-P." } ], "journal": "Bioinformatics" } }, { "doi": "10.1101/pdb.prot5634", "pmid": "21632777", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "IMGT/junctionanalysis: IMGT standardized analysis of the V-J and V-D-J junctions of the rearranged immunoglobulins (IG) and T cell receptors (TR)", "abstract": "", "date": "2011-06-01T00:00:00Z", "citationCount": 89, "authors": [ { "name": "Giudicelli V." }, { "name": "Lefranc M.-P." } ], "journal": "Cold Spring Harbor Protocols" } }, { "doi": "10.1093/nar/gku1056", "pmid": "25378316", "pmcid": "PMC4383898", "type": [], "version": null, "note": null, "metadata": { "title": "IMGT R, the international ImMunoGeneTics information system R 25 years on", "abstract": "IMGT, the international ImMunoGeneTics information system (http://www.imgt.org) is the global reference in immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), IMGT marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) and proteins of the IgSF and MhSF superfamilies. IMGT is built on the IMGTONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and 3D structures. The concepts include the IMGTR standardized keywords (identification), IMGTR standardized labels (description), IMGTR standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGTR comprises 7 databases, 17 online tools and 15 000 pages of web resources, and provides a high-quality and integrated system for analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses, including NGS high-throughput data. Tools and databases are used in basic, veterinary and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. The IMGT/mAb-DB interface was developed for therapeutic antibodies and fusion proteins for immunological applications (FPIA). IMGTR is freely available at http://www.imgt.org.", "date": "2015-01-28T00:00:00Z", "citationCount": 402, "authors": [ { "name": "Lefranc M.-P." }, { "name": "Giudicelli V." }, { "name": "Duroux P." }, { "name": "Jabado-Michaloud J." }, { "name": "Folch G." }, { "name": "Aouinti S." }, { "name": "Carillon E." }, { "name": "Duvergey H." }, { "name": "Houles A." }, { "name": "Paysan-Lafosse T." }, { "name": "Hadi-Saljoqi S." }, { "name": "Sasorith S." }, { "name": "Lefranc G." }, { "name": "Kossida S." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Véronique Giudicelli", "email": "veronique.giudicelli@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Patrice Duroux", "email": "patrice.duroux@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Marie-Paule Lefranc", "email": "marie-paule.lefranc@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Sofia Kossida", "email": "sofia.kossida@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "vgiudicelli", "additionDate": "2019-12-18T08:05:57Z", "lastUpdate": "2024-11-25T13:59:28.822742Z", "editPermission": { "type": "group", "authors": [ "skossida", "pduroux", "Joumana", "geraldine.folch", "vgiudicelli" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "IMGT PhyloGene", "description": "IMGT/PhyloGene is the IMGT® tool to compute and draw phylogenetic trees for immunoglobulin (IG) and T cell receptor (TR) V-REGION nucleotide sequences.\nAnalysis is based on the IMGT-ONTOLOGY concepts.", "homepage": "http://www.imgt.org/IMGTPhylogeny/", "biotoolsID": "IMGT_PhyloGene", "biotoolsCURIE": "biotools:IMGT_PhyloGene", "version": [], "otherID": [], "relation": [ { "biotoolsID": "imgt", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0499", "term": "Tree-based sequence alignment" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2299", "term": "Gene name" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2858", "term": "Ontology concept" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2523", "term": "Phylogenetic data" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_0867", "term": "Sequence alignment report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3948", "term": "Immunoinformatics" }, { "uri": "http://edamontology.org/topic_3930", "term": "Immunogenetics" } ], "operatingSystem": [], "language": [ "Perl" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.imgt.org/IMGTPhylogeny/html/IMGTPhylogenyDoc.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/s0145-305x(03)00078-8", "pmid": "12818634", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "IMGT/PhyloGene: An on-line tool for comparative analysis of immunoglobulin and T cell receptor genes", "abstract": "IMGT/PhyloGene is an on-line software package for comparative analysis of immunoglobulin (IG) and T cell receptor (TR) variable genes of all vertebrate species, newly implemented in IMGT, the international ImMunoGeneTics information system ®. IMGT/PhyloGene is strongly associated with the IMGT gene and allele nomenclature and with the IMGT unique numbering for V-REGION, which directly creates standardized alignments from IMGT reference sequences. IMGT/PhyloGene is the first tool to use the IMGT expertized and standardized data for automated comparative analyses, and the first on-line software package for phylogenetic reconstruction to be integrated to a sequence database. Starting from a standardized alignment of selected sequences, IMGT/PhyloGene computes a matrix of evolutionary distances, builds a tree using the Neighbor-Joining (NJ) algorithm, and outputs various graphical tree representations. The resulting IMGT/PhyloGene tree is then used as a support for studying the evolution of particular subregions, such as the CDR-IMGT (Complementarity Determining Regions) or the V-RS (Variable gene Recombination Signals). IMGT/PhyloGene is freely available at http://imgt.cines.fr. © 2003 Elsevier Science Ltd. All rights reserved.", "date": "2003-01-01T00:00:00Z", "citationCount": 37, "authors": [ { "name": "Elemento O." }, { "name": "Lefranc M.-P." } ], "journal": "Developmental and Comparative Immunology" } }, { "doi": "10.1093/nar/gku1056", "pmid": "25378316", "pmcid": "PMC4383898", "type": [], "version": null, "note": null, "metadata": { "title": "IMGT R, the international ImMunoGeneTics information system R 25 years on", "abstract": "IMGT, the international ImMunoGeneTics information system (http://www.imgt.org) is the global reference in immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), IMGT marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) and proteins of the IgSF and MhSF superfamilies. IMGT is built on the IMGTONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and 3D structures. The concepts include the IMGTR standardized keywords (identification), IMGTR standardized labels (description), IMGTR standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGTR comprises 7 databases, 17 online tools and 15 000 pages of web resources, and provides a high-quality and integrated system for analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses, including NGS high-throughput data. Tools and databases are used in basic, veterinary and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. The IMGT/mAb-DB interface was developed for therapeutic antibodies and fusion proteins for immunological applications (FPIA). IMGTR is freely available at http://www.imgt.org.", "date": "2015-01-28T00:00:00Z", "citationCount": 402, "authors": [ { "name": "Lefranc M.-P." }, { "name": "Giudicelli V." }, { "name": "Duroux P." }, { "name": "Jabado-Michaloud J." }, { "name": "Folch G." }, { "name": "Aouinti S." }, { "name": "Carillon E." }, { "name": "Duvergey H." }, { "name": "Houles A." }, { "name": "Paysan-Lafosse T." }, { "name": "Hadi-Saljoqi S." }, { "name": "Sasorith S." }, { "name": "Lefranc G." }, { "name": "Kossida S." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Patrice Duroux", "email": "patrice.duroux@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Marie-Paule Lefranc", "email": "marie-paule.lefranc@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Sofia Kossida", "email": "sofia.kossida@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "vgiudicelli", "additionDate": "2019-12-20T13:29:52Z", "lastUpdate": "2024-11-25T13:59:18.263208Z", "editPermission": { "type": "group", "authors": [ "Joumana", "pduroux", "geraldine.folch", "skossida" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "IMGT V-QUEST", "description": "IMGT/V-QUEST is the IMGT® tool for nucleotide sequence alignment and analysis of immunoglobulin (IG) or antibody and T cell receptor (TR) variable domains, integrates IMGT/JunctionAnalysis, IMGT/Automat and IMGT/Collier-de-Perles.\nAnalysis is based on the IMGT-ONTOLOGY concepts.", "homepage": "http://www.imgt.org/IMGT_vquest", "biotoolsID": "imgt_v-quest", "biotoolsCURIE": "biotools:imgt_v-quest", "version": [], "otherID": [], "relation": [ { "biotoolsID": "imgt", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" }, { "uri": "http://edamontology.org/operation_0258", "term": "Sequence alignment analysis" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" }, { "uri": "http://edamontology.org/operation_0448", "term": "Sequence alignment analysis (conservation)" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3948", "term": "Immunoinformatics" }, { "uri": "http://edamontology.org/topic_3930", "term": "Immunogenetics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.imgt.org/IMGT_vquest/user_guide", "type": [ "User manual" ], "note": null }, { "url": "http://www.imgt.org/IMGT_vquest/program_versions", "type": [ "Release notes" ], "note": "IMGT/V-QUEST program versions" }, { "url": "http://www.imgt.org/IMGT_vquest/data_releases", "type": [ "Release notes" ], "note": "IMGT/V-QUEST reference directory releases" } ], "publication": [ { "doi": "10.1093/nar/gkn316", "pmid": "18503082", "pmcid": "PMC2447746", "type": [], "version": null, "note": null, "metadata": { "title": "IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis.", "abstract": "IMGT/V-QUEST is the highly customized and integrated system for the standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. IMGT/V-QUEST identifies the variable (V), diversity (D) and joining (J) genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. New functionalities were added through a complete rewrite in Java. IMGT/V-QUEST analyses batches of sequences (up to 50) in a single run. IMGT/V-QUEST describes the V-REGION mutations and identifies the hot spot positions in the closest germline V gene. IMGT/V-QUEST can detect insertions and deletions in the submitted sequences by reference to the IMGT unique numbering. IMGT/V-QUEST integrates IMGT/JunctionAnalysis for a detailed analysis of the V-J and V-D-J junctions, and IMGT/Automat for a full V-J- and V-D-J-REGION annotation. IMGT/V-QUEST displays, in 'Detailed view', the results and alignments for each submitted sequence individually and, in 'Synthesis view', the alignments of the sequences that, in a given run, express the same V gene and allele. The 'Advanced parameters' allow to modify default parameters used by IMGT/V-QUEST and IMGT/JunctionAnalysis according to the users' interest. IMGT/V-QUEST is freely available for academic research at http://imgt.cines.fr.", "date": "2008-01-01T00:00:00Z", "citationCount": 942, "authors": [ { "name": "Brochet X." }, { "name": "Lefranc M.P." }, { "name": "Giudicelli V." } ], "journal": "Nucleic acids research" } }, { "doi": "10.1093/nar/gkh412", "pmid": "15215425", "pmcid": "PMC441550", "type": [], "version": null, "note": null, "metadata": { "title": "IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis", "abstract": "IMGT/V-QUEST, for 'V-QUEry and STandardization', is an integrated software program which analyses the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. The extraordinary diversity of the IG and TR repertoires (1012 antibodies and 1012 TR per individual) results from several mechanisms at the DNA level: the combinatorial diversity of the variable (V), diversity (D) and joining (J) genes, the N-diversity and, for IG, the somatic mutations. IMGT/V-QUEST identifies the V, D and J genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. IMGT/V-QUEST delimits the structurally important features, frameworks and complementarity-determining regions (the last of these forming the antigen binding site), on the basis of the IMGT unique numbering. The tool localizes the somatic mutations of the IG rearranged sequences. IMGT/V-QUEST also dynamically displays a graphical two-dimensional representation, or IMGT Collier de Peries, of the IG and TR variable regions. Moreover, IMGT/V-QUEST can interact with IMGT/JunctionAnalysis for the detailed description of the V-J and V-D-J junctions, and with IMGT/PhyloGene for the construction of phylogenetic trees. IMGT/V-QUEST is currently available for human and mouse, and partly for non-human primates, sheep, chondrichthyes and teleostei. IMGT/V-QUEST is freely available at http://imgt.cines.fri. © Oxford University Press 2004; all rights reserved.", "date": "2004-07-01T00:00:00Z", "citationCount": 253, "authors": [ { "name": "Giudicelli V." }, { "name": "Chaume D." }, { "name": "Lefranc M.-P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1101/pdb.prot5633", "pmid": "21632778", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "IMGT/V-QUEST: IMGT standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences", "abstract": "", "date": "2011-06-01T00:00:00Z", "citationCount": 301, "authors": [ { "name": "Giudicelli V." }, { "name": "Brochet X." }, { "name": "Lefranc M.-P." } ], "journal": "Cold Spring Harbor Protocols" } }, { "doi": "10.1093/nar/gku1056", "pmid": "25378316", "pmcid": "PMC4383898", "type": [], "version": null, "note": null, "metadata": { "title": "IMGT R, the international ImMunoGeneTics information system R 25 years on", "abstract": "IMGT, the international ImMunoGeneTics information system (http://www.imgt.org) is the global reference in immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), IMGT marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) and proteins of the IgSF and MhSF superfamilies. IMGT is built on the IMGTONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and 3D structures. The concepts include the IMGTR standardized keywords (identification), IMGTR standardized labels (description), IMGTR standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGTR comprises 7 databases, 17 online tools and 15 000 pages of web resources, and provides a high-quality and integrated system for analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses, including NGS high-throughput data. Tools and databases are used in basic, veterinary and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. The IMGT/mAb-DB interface was developed for therapeutic antibodies and fusion proteins for immunological applications (FPIA). IMGTR is freely available at http://www.imgt.org.", "date": "2015-01-28T00:00:00Z", "citationCount": 402, "authors": [ { "name": "Lefranc M.-P." }, { "name": "Giudicelli V." }, { "name": "Duroux P." }, { "name": "Jabado-Michaloud J." }, { "name": "Folch G." }, { "name": "Aouinti S." }, { "name": "Carillon E." }, { "name": "Duvergey H." }, { "name": "Houles A." }, { "name": "Paysan-Lafosse T." }, { "name": "Hadi-Saljoqi S." }, { "name": "Sasorith S." }, { "name": "Lefranc G." }, { "name": "Kossida S." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Marie-Paule Lefranc", "email": "Marie-Paule.Lefranc@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Véronique Giudicelli", "email": "veronique.giudicelli@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Patrice Duroux", "email": "patrice.duroux@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Sofia Kossida", "email": "sofia.kossida@igh.cnrs.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "vgiudicelli", "additionDate": "2017-05-01T13:19:16Z", "lastUpdate": "2024-11-25T13:59:09.724903Z", "editPermission": { "type": "group", "authors": [ "Shengli", "vgiudicelli", "skossida", "pduroux", "Joumana", "geraldine.folch" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }
