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{ "count": 123, "next": "?page=2", "previous": null, "list": [ { "name": "Jalview", "description": "Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. 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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. 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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. 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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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It is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs from Jalview.", "homepage": "http://www.compbio.dundee.ac.uk/jabaws", "biotoolsID": "clustalo_ws_jabaws", "biotoolsCURIE": "biotools:clustalo_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": [ { "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_1929", "term": "FASTA" } ] } ], "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": [ "clustal", "JABAWS" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.biocatalogue.org/services/3687", "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/ClustalOWS.html", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btr304", "pmid": "21593132", "pmcid": "PMC3129525", "type": [ "Primary" ], "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. 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. Published by Oxford University Press.", "date": "2011-07-01T00:00:00Z", "citationCount": 96, "authors": [ { "name": "Troshin P.V." }, { "name": "Procter J.B." }, { "name": "Barton G.J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "BioCatalogue", "email": null, "url": "https://www.biocatalogue.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Documentor" ], "note": null }, { "name": null, "email": null, "url": "http://www.compbio.dundee.ac.uk/jabaws/contacts.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "BioCatalogue", "additionDate": "2015-08-03T09:36:06Z", "lastUpdate": "2024-11-25T14:17:59.498371Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Clustal WS (jabaws)", "description": "Finds the best global alignment for a set of input sequences (nucleic acid or protein).", "homepage": "http://www.compbio.dundee.ac.uk/jabaws/", "biotoolsID": "clustal_ws_jabaws", "biotoolsCURIE": "biotools:clustal_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": [ { "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_1929", "term": "FASTA" } ] } ], "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": [ "clustal", "JABAWS" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.biocatalogue.org/services/3760", "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/ClustalWS.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. 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. Published by Oxford University Press.", "date": "2011-07-01T00:00:00Z", "citationCount": 96, "authors": [ { "name": "Troshin P.V." }, { "name": "Procter J.B." }, { "name": "Barton G.J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "BioCatalogue", "email": null, "url": "https://www.biocatalogue.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Documentor" ], "note": null }, { "name": null, "email": null, "url": "http://www.compbio.dundee.ac.uk/jabaws/contacts.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "BioCatalogue", "additionDate": "2015-08-03T09:36:11Z", "lastUpdate": "2024-11-25T14:17:56.987631Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "T-Coffee", "description": "A multiple sequence alignment package that can be used for DNA, RNA and protein sequences. It can be used to align sequences or to combine the output of other alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment.", "homepage": "http://www.tcoffee.org/Projects/tcoffee/", "biotoolsID": "tcoffee", "biotoolsCURIE": "biotools:tcoffee", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "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": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-3.0", "collectionID": [ "T-Coffee" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.biocatalogue.org/services/3720", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://www.tcoffee.org/Projects/tcoffee/#DOWNLOAD", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.tcoffee.org/Projects/tcoffee/", "type": [ "General" ], "note": null }, { "url": "http://www.tcoffee.org/Projects/tcoffee/#INSTALLATION", "type": [ "Installation instructions" ], "note": null }, { "url": "http://www.tcoffee.org/Projects/tcoffee/documentation/README", "type": [ "General" ], "note": "T-Coffee README file" }, { "url": "http://www.tcoffee.org/Projects/tcoffee/#FAQ", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1006/jmbi.2000.4042", "pmid": "10964570", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "T-coffee: A novel method for fast and accurate multiple sequence alignment", "abstract": "We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives. 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. 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. Published by Oxford University Press.", "date": "2011-07-01T00:00:00Z", "citationCount": 96, "authors": [ { "name": "Troshin P.V." }, { "name": "Procter J.B." }, { "name": "Barton G.J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "BioCatalogue", "email": null, "url": "https://www.biocatalogue.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Documentor" ], "note": null }, { "name": null, "email": null, "url": "http://www.compbio.dundee.ac.uk/jabaws/contacts.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "BioCatalogue", "additionDate": "2015-08-03T09:36:10Z", "lastUpdate": "2024-11-25T14:17:47.947650Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BWA", "description": "Fast, accurate, memory-efficient aligner for short and long sequencing reads", "homepage": "http://bio-bwa.sourceforge.net", "biotoolsID": "bwa", "biotoolsCURIE": "biotools:bwa", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3211", "term": "Genome indexing" } ], "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_3210", "term": "Genome index" }, "format": [] } ], "note": "Index database sequences in the FASTA format. database", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3210", "term": "Genome index" }, "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_1916", "term": "Alignment" }, "format": [] } ], "note": "Align 70bp-1Mbp query sequences with the BWA-MEM algorithm. 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. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license.", "date": "2016-01-01T00:00:00Z", "citationCount": 1097, "authors": [ { "name": "Yates A." }, { "name": "Akanni W." }, { "name": "Amode M.R." }, { "name": "Barrell D." }, { "name": "Billis K." }, { "name": "Carvalho-Silva D." }, { "name": "Cummins C." }, { "name": "Clapham P." }, { "name": "Fitzgerald S." }, { "name": "Gil L." }, { "name": "Giron C.G." }, { "name": "Gordon L." }, { "name": "Hourlier T." }, { "name": "Hunt S.E." }, { "name": "Janacek S.H." }, { "name": "Johnson N." }, { "name": "Juettemann T." }, { "name": "Keenan S." }, { "name": "Lavidas I." }, { "name": "Martin F.J." }, { "name": "Maurel T." }, { "name": "McLaren W." }, { "name": "Murphy D.N." }, { "name": "Nag R." }, { "name": "Nuhn M." }, { "name": "Parker A." }, { "name": "Patricio M." }, { "name": "Pignatelli M." }, { "name": "Rahtz M." }, { "name": "Riat H.S." }, { "name": "Sheppard D." }, { "name": "Taylor K." }, { "name": "Thormann A." }, { "name": "Vullo A." }, { "name": "Wilder S.P." }, { "name": "Zadissa A." }, { "name": "Birney E." }, { "name": "Harrow J." }, { "name": "Muffato M." }, { "name": "Perry E." }, { "name": "Ruffier M." }, { "name": "Spudich G." }, { "name": "Trevanion S.J." }, { "name": "Cunningham F." }, { "name": "Aken B.L." }, { "name": "Zerbino D.R." }, { "name": "Flicek P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Ensembl team", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "helpdesk@ensemblgenomes.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ensembl Genomes webteam", "email": "eg-webteam@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI", "additionDate": "2015-01-29T15:47:59Z", "lastUpdate": "2024-11-25T14:07:17.756843Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Ensembl Genomes Plants Blast", "description": "Search Ensembl Plants sequences with WU-BLAST.", "homepage": "http://plants.ensembl.org/Multi/blastview", "biotoolsID": "ensembl_genomes_plants_blast", "biotoolsCURIE": "biotools:ensembl_genomes_plants_blast", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "blast", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" }, { "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" } ] } ], "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://plants.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. The webserver can be found at: http://genome.ku.dk/resources/war.", "date": "2008-01-01T00:00:00Z", "citationCount": 41, "authors": [ { "name": "Torarinsson E." }, { "name": "Lindgreen S." } ], "journal": "Nucleic acids research" } } ], "credit": [ { "name": "binf.ku.dk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Stinus Lindgreen", "email": "stinus@binf.ku.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2015-07-28T11:14:46Z", "lastUpdate": "2024-11-25T14:06:15.464725Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "IMGT 2Dstructure-DB", "description": "IMGT/2Dstructure-DB is the IMGT® database for 2D structures (IMGT Colliers de Perles) of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins and related proteins of the immune system (RPI).\nAnnotation is based on the IMGT-ONTOLOGY concepts.", "homepage": "http://www.imgt.org/3Dstructure-DB/", "biotoolsID": "IMGT_2Dstructure-DB", "biotoolsCURIE": "biotools:IMGT_2Dstructure-DB", "version": [], "otherID": [], "relation": [ { "biotoolsID": "imgt", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_2416", "term": "Protein secondary structure analysis" } ], "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" } ] } ], "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_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_3930", "term": "Immunogenetics" }, { "uri": "http://edamontology.org/topic_3948", "term": "Immunoinformatics" } ], "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": [ { "url": "http://www.imgt.org/3Dstructure-DB/doc/IMGT3DstructureDBHelp.shtml", "type": [ "User manual" ], "note": null } ], "publication": [ { "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 } ], "owner": "skossida", "additionDate": "2019-12-20T15:37:44Z", "lastUpdate": "2024-11-25T14:00:19.591199Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, 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"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 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 }, { "name": "Clustal 1.8 (Clustal W, Clustal X)", "description": "Multiple sequence alignment software. Old deprecated versions. Even older versions were CLUSTAL and CLUSTAL V (ClustalV).", "homepage": "http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/", "biotoolsID": "clustalw", "biotoolsCURIE": "biotools:clustalw", "version": [ "1.8 - 1.83" ], "otherID": [], "relation": [ { "biotoolsID": "clustal2", "type": "hasNewVersion" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "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": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "clustal" ], "maturity": "Legacy", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/", "type": "Downloads page", "note": "Archived old versions.", "version": "1.8 - 1.83" } ], "documentation": [], "publication": [ { "doi": "10.1093/nar/22.22.4673", "pmid": "7984417", "pmcid": "PMC308517", "type": [ "Primary" ], "version": "historical CLUSTAL W", "note": "Historical publication on CLUSTAL W. Open access to PDF only.", "metadata": { "title": "CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice", "abstract": "The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to downweight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available. © 1994 Oxford University Press.", "date": "1994-11-11T00:00:00Z", "citationCount": 58068, "authors": [ { "name": "Thompson J.D." }, { "name": "Higgins D.G." }, { "name": "Gibson T.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/25.24.4876", "pmid": "9396791", "pmcid": "PMC147148", "type": [ "Primary" ], "version": "historical CLUSTAL X", "note": "Historical publication on CLUSTAL X. Open access.", "metadata": { "title": "The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools", "abstract": "CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.", "date": "1997-12-15T00:00:00Z", "citationCount": 36458, "authors": [ { "name": "Thompson J.D." }, { "name": "Gibson T.J." }, { "name": "Plewniak F." }, { "name": "Jeanmougin F." }, { "name": "Higgins D.G." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkg500", "pmid": "12824352", "pmcid": "PMC168907", "type": [ "Primary" ], "version": "1.83", "note": "Short overview article, with some new features of Clustal, Clustal X, and other associated software nad services. Open access.", "metadata": { "title": "Multiple sequence alignment with the Clustal series of programs", "abstract": "The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (http://www.ebi.ac.uk/clustalw/).", "date": "2003-07-01T00:00:00Z", "citationCount": 4217, "authors": [ { "name": "Chenna R." }, { "name": "Sugawara H." }, { "name": "Koike T." }, { "name": "Lopez R." }, { "name": "Gibson T.J." }, { "name": "Higgins D.G." }, { "name": "Thompson J.D." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/bioinformatics/8.2.189", "pmid": "1591615", "pmcid": null, "type": [ "Other" ], "version": "historical CLUSTAL", "note": "Historical publication on CLUSTAL. Closed access.", "metadata": { "title": "CLUSTAL V: Improved software for multiple sequence alignment", "abstract": "The CLUSTAL package of multiple sequence alignment programs has been completely rewritten and many new features added. The new software is a single program called CLUSTAL V, which is written in C and can be used on standard C compiler. The main new features are the ability to store and reuse old alignments and the ability to calculate phylogenetic trees after alignment. The program is simple to use, completely menu driven and on-line help is provided. © 1992 Oxford University Press.", "date": "1992-04-01T00:00:00Z", "citationCount": 2572, "authors": [ { "name": "Higgins D.G." }, { "name": "Bleasby A.J." }, { "name": "Fuchs R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1016/0378-1119(88)90330-7", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": "historical CLUSTAL", "note": "Historical publication on CLUSTAL. Closed access.", "metadata": { "title": "CLUSTAL: a package for performing multiple sequence alignment on a microcomputer", "abstract": "An approach for performing multiple alignments of large numbers of amino acid or nucleotide sequences is described. The method is based on first deriving a phylogenetic tree from a matrix of all pairwise sequence similarity scores, obtained using a fast pairwise alignment algorithm. Then the multiple alignment is achieved from a series of pairwise alignments of clusters of sequences, following the order of branching in the tree. The method is sufficiently fast and economical with memory to be easily implemented on a microcomputer, and yet the results obtained are comparable to those from packages requiring mainframe computer facilities. © 1988.", "date": "1988-12-15T00:00:00Z", "citationCount": 3024, "authors": [ { "name": "Higgins D.G." }, { "name": "Sharp P.M." } ], "journal": "Gene" } } ], "credit": [ { "name": "Clustal helpdesk", "email": "clustalw@ucd.ie", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-03-24T09:34:04Z", "lastUpdate": "2024-11-25T13:59:02.403313Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ProteinsPlus", "description": "It supports various commonly required tasks of structure-based molecular modeling. It provides functionalities for structure quality assessment , hydrogen placement, the search for alternative conformations, the generation of 2D-interaction diagrams, protein-protein interface classification as well as automatic pocket detection and druggablity assessment.", "homepage": "http://proteinsplus.zbh.uni-hamburg.de", "biotoolsID": "proteinsplus", "biotoolsCURIE": "biotools:proteinsplus", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0321", "term": "Protein model validation" }, { "uri": "http://edamontology.org/operation_2949", "term": "Protein interaction analysis" }, { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_2575", "term": "Protein binding site prediction" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/operation_0339", "term": "Structure database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_0897", "term": "Protein property" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2992", "term": "Protein structure image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1208", "term": "protein" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_3534", "term": "Protein binding sites" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "de.NBI", "COVID-19" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "http://proteinsplus.zbh.uni-hamburg.de/help/index", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkx333", "pmid": "28472372", "pmcid": "PMC5570178", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Proteins Plus: A web portal for structure analysis of macromolecules", "abstract": "With currently more than 126 000 publicly available structures and an increasing growth rate, the Protein Data Bank constitutes a rich data source for structure-driven research in fields like drug discovery, crop science and biotechnology in general. Typical workflows in these areas involve manifold computational tools for the analysis and prediction of molecular functions. Here, we present the ProteinsPlus web server that offers a unified easy-to-use interface to a broad range of tools for the early phase of structure-based molecular modeling. This includes solutions for commonly required pre-processing tasks like structure quality assessment (EDIA), hydrogen placement (Protoss) and the search for alternative conformations (SIENA). Beyond that, it also addresses frequent problems as the generation of 2D-interaction diagrams (PoseView), protein-protein interface classification (HyPPI) as well as automatic pocket detection and druggablity assessment (DoGSiteScorer). The unified ProteinsPlus interface covering all featured approaches provides various facilities for intuitive input and result visualization, case-specific parameterization and download options for further processing. Moreover, its generalized workflow allows the user a quick familiarization with the different tools. ProteinsPlus also stores the calculated results temporarily for future request and thus facilitates convenient result communication and re-access.", "date": "2017-07-03T00:00:00Z", "citationCount": 167, "authors": [ { "name": "Fahrrolfes R." }, { "name": "Bietz S." }, { "name": "Flachsenberg F." }, { "name": "Meyder A." }, { "name": "Nittinger E." }, { "name": "Otto T." }, { "name": "Volkamer A." }, { "name": "Rarey M." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkaa235", "pmid": "32297936", "pmcid": "PMC7319454", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ProteinsPlus: Interactive analysis of protein–ligand binding interfaces", "abstract": "Due to the increasing amount of publicly available protein structures searching, enriching and investigating these data still poses a challenging task. The ProteinsPlus web service (https://proteins.plus) offers a broad range of tools addressing these challenges. The web interface to the tool collection focusing on protein–ligand interactions has been geared towards easy and intuitive access to a large variety of functionality for life scientists. Since our last publication, the ProteinsPlus web service has been extended by additional services as well as it has undergone substantial infrastructural improvements. A keyword search functionality was added on the start page of ProteinsPlus enabling users to work on structures without knowing their PDB code. The tool collection has been augmented by three tools: StructureProfiler validates ligands and active sites using selection criteria of well-established protein–ligand benchmark data sets, WarPP places water molecules in the lig- and binding sites of a protein, and METALizer calculates, predicts and scores coordination geometries of metal ions based on surrounding complex atoms. Additionally, all tools provided by ProteinsPlus are available through a REST service enabling the automated integration in structure processing and modeling pipelines.", "date": "2020-01-01T00:00:00Z", "citationCount": 164, "authors": [ { "name": "Schoning-Stierand K." }, { "name": "Diedrich K." }, { "name": "Fahrrolfes R." }, { "name": "Flachsenberg F." }, { "name": "Meyder A." }, { "name": "Nittinger E." }, { "name": "Steinegger R." }, { "name": "Rarey M." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "University of Hamburg - Center for Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": null, "email": "rarey-office@zbh.uni-hamburg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "stierand", "additionDate": "2017-08-01T11:05:01Z", "lastUpdate": "2024-11-25T13:58:14.662890Z", "editPermission": { "type": "group", "authors": [ "Bietz" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "setuppromoter", "description": "Builds a fasta file of sequences from a reference genome using promoter region coordinates.", "homepage": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/promoteur_tools/setuppromoter/1.0", "biotoolsID": "setuppromoter", "biotoolsCURIE": "biotools:setuppromoter", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0749", "term": "Transcription factors and regulatory sites" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [ "galaxyPasteur", "Institut Pasteur" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/promoteur_tools/setuppromoter/1.0", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr%2Frepos%2Ffmareuil%2Fpromoteur_tools%2Fsetuppromoter%2F1.0", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": "27137889", "pmcid": "PMC4987906", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. 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particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1410, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Kuster G.V." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:22:35Z", "lastUpdate": "2024-11-25T13:51:15.191252Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "crop", "description": "A clustering tool which clusters 16S rRNA sequences into Operational Taxonomic Units (OTU).", "homepage": "https://code.google.com/archive/p/crop-tingchenlab/", "biotoolsID": "crop", "biotoolsCURIE": "biotools:crop", "version": [ "1.33" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0291", "term": "Sequence clustering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "galaxyPasteur" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/afelten/microbiome_analyses/CROP/1.33", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/btq725", "pmid": "21233169", "pmcid": "PMC3042185", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Clustering 16S rRNA for OTU prediction: A method of unsupervised Bayesian clustering", "abstract": "Motivation: With the advancements of next-generation sequencing technology, it is now possible to study samples directly obtained from the environment. Particularly, 16S rRNA gene sequences have been frequently used to profile the diversity of organisms in a sample. However, such studies are still taxed to determine both the number of operational taxonomic units (OTUs) and their relative abundance in a sample. Results: To address these challenges, we propose an unsupervised Bayesian clustering method termed Clustering 16S rRNA for OTU Prediction (CROP). CROP can find clusters based on the natural organization of data without setting a hard cut-off threshold (3%/5%) as required by hierarchical clustering methods. By applying our method to several datasets, we demonstrate that CROP is robust against sequencing errors and that it produces more accurate results than conventional hierarchical clustering methods. © The Author(s) 2011. Published by Oxford University Press.", "date": "2011-03-01T00:00:00Z", "citationCount": 208, "authors": [ { "name": "Hao X." }, { "name": "Jiang R." }, { "name": "Chen T." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/nar/gkw343", "pmid": "27137889", "pmcid": "PMC4987906", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1410, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Kuster G.V." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:27:49Z", "lastUpdate": "2024-11-25T13:50:16.456270Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "noisy", "description": "Cleaning aligned sequences.", "homepage": "http://www.bioinf.uni-leipzig.de/Software/noisy/", "biotoolsID": "noisy", "biotoolsCURIE": "biotools:noisy", "version": [ "1.5.12.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3081", "term": "Sequence alignment editing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3466", "term": "EPS" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C++" ], "license": null, "collectionID": [ "galaxyPasteur" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/noisy/noisy/1.5.12.1", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.bioinf.uni-leipzig.de/Software/noisy/noisy.1.html#lbAD", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/1748-7188-3-7", "pmid": "18577231", "pmcid": "PMC2464588", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Noisy: Identification of problematic columns in multiple sequence alignments", "abstract": "Motivation: Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of (i) phylogenetically informative and (ii) effectively randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction. Results: We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of \"tree quality\". In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters. Software: The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1) the average bootstrap support obtained from the original alignment is low, and (2) there are sufficiently many taxa in the data set - at least, say, 12 to 15 taxa. The software can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/noisy/. © 2008 Dress et al; licensee BioMed Central Ltd.", "date": "2008-06-24T00:00:00Z", "citationCount": 116, "authors": [ { "name": "Dress A.W.M." }, { "name": "Flamm C." }, { "name": "Fritzsch G." }, { "name": "Grunewald S." }, { "name": "Kruspe M." }, { "name": "Prohaska S.J." }, { "name": "Stadler P.F." } ], "journal": "Algorithms for Molecular Biology" } }, { "doi": "10.1093/nar/gkw343", "pmid": "27137889", "pmcid": "PMC4987906", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1410, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Kuster G.V." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:26:05Z", "lastUpdate": "2024-11-25T13:48:48.576677Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "noisy_oneclick", "description": "Cleaning aligned sequences.", "homepage": "http://www.bioinf.uni-leipzig.de/Software/noisy/", "biotoolsID": "noisy_oneclick", "biotoolsCURIE": "biotools:noisy_oneclick", "version": [ "1.5.12.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0258", "term": "Sequence alignment analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "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_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_3466", "term": "EPS" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/oneclick_phylogeny/noisy_oneclick/1.5.12.1", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": "27137889", "pmcid": "PMC4987906", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1410, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Kuster G.V." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:28:29Z", "lastUpdate": "2024-11-25T13:47:41.857256Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "gblocks_oneclick", "description": "Cleaning aligned sequences.", "homepage": "http://www.embl-heidelberg.de/~castresa/Gblocks/Gblocks.html", "biotoolsID": "gblocks_oneclick", "biotoolsCURIE": "biotools:gblocks_oneclick", "version": [ "0.91.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0258", "term": "Sequence alignment analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "galaxyPasteur", "gblocks" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/oneclick_phylogeny/gblocks_oneclick/0.91.1", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkw343", "pmid": "27137889", "pmcid": "PMC4987906", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale.", "date": "2016-07-08T00:00:00Z", "citationCount": 1410, "authors": [ { "name": "Afgan E." }, { "name": "Baker D." }, { "name": "van den Beek M." }, { "name": "Blankenberg D." }, { "name": "Bouvier D." }, { "name": "Cech M." }, { "name": "Chilton J." }, { "name": "Clements D." }, { "name": "Coraor N." }, { "name": "Eberhard C." }, { "name": "Gruning B." }, { "name": "Guerler A." }, { "name": "Hillman-Jackson J." }, { "name": "Kuster G.V." }, { "name": "Rasche E." }, { "name": "Soranzo N." }, { "name": "Turaga N." }, { "name": "Taylor J." }, { "name": "Nekrutenko A." }, { "name": "Goecks J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Galaxy Support Team", "email": "galaxy@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:24:43Z", "lastUpdate": "2024-11-25T13:47:39.381701Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "T-Coffee API (EBI)", "description": "Multiple sequence alignment program. The main characteristic is that it will allow you to combine results obtained with several alignment methods.", "homepage": "http://www.ebi.ac.uk/Tools/webservices/services/msa/tcoffee_rest", "biotoolsID": "TCoffee_API_EBI", "biotoolsCURIE": "biotools:TCoffee_API_EBI", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "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 API" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "T-Coffee" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.biocatalogue.org/services/3137", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/Tools/webservices/services/msa/tcoffee_rest", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1006/jmbi.2000.4042", "pmid": "10964570", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "T-coffee: A novel method for fast and accurate multiple sequence alignment", "abstract": "We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives. 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. 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VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was developed for the 1000 Genomes Project, and has also been adopted by other projects such as UK10K, dbSNP and the NHLBI Exome Project. VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. © The Author(s) 2011. Published by Oxford University Press.", "date": "2011-08-01T00:00:00Z", "citationCount": 9374, "authors": [ { "name": "Danecek P." }, { "name": "Auton A." }, { "name": "Abecasis G." }, { "name": "Albers C.A." }, { "name": "Banks E." }, { "name": "DePristo M.A." }, { "name": "Handsaker R.E." }, { "name": "Lunter G." }, { "name": "Marth G.T." }, { "name": "Sherry S.T." }, { "name": "McVean G." }, { "name": "Durbin R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/nar/gkw343", "pmid": "27137889", "pmcid": "PMC4987906", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update", "abstract": "High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. 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