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It integrates for each species: \ni) a main knowledge base with extended functional, gene expression, phenotyping, anatomical and phylogenetic information; \nii) A multispecies genomic browser; \niii) a Genomicus gene synteny browser.", "homepage": "https://www.aniseed.fr", "biotoolsID": "ANISEED", "biotoolsCURIE": "biotools:ANISEED", "version": [ "2019" ], "otherID": [ { "value": "DOI:10.1093/nar/gkx1108", "type": "doi", "version": "2017" }, { "value": "DOI:10.1093/nar/gkv966", "type": "doi", "version": "2015" }, { "value": "DOI:10.1101/gr.108175.110", "type": "doi", "version": "2010" }, { "value": "DOI:10.1016/j.cub.2005.12.044", "type": "doi", "version": "2006" } ], "relation": [ { "biotoolsID": "interpro", "type": "uses" }, { "biotoolsID": "blast", "type": "uses" }, { "biotoolsID": "genomicus-tunicates", "type": "uses" }, { "biotoolsID": "ciona_robusta_anatomy_and_development_ontology", "type": "uses" }, { "biotoolsID": "ciona_robusta_anatomy_and_development_ontology", "type": "includes" }, { "biotoolsID": "go", "type": "uses" }, { "biotoolsID": "morphonet", "type": "uses" }, { "biotoolsID": "morphonet", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0567", "term": "Phylogenetic tree visualisation" }, { "uri": "http://edamontology.org/operation_3208", "term": "Genome visualisation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" }, { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" }, { "uri": "http://edamontology.org/operation_2495", "term": "Expression analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2042", "term": "Evidence" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2042", "term": "Evidence" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Ontology", "Web API", "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3064", "term": "Developmental biology" }, { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" }, { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" }, { "uri": "http://edamontology.org/topic_3065", "term": "Embryology" }, { "uri": "http://edamontology.org/topic_3383", "term": "Biological imaging" }, { "uri": "http://edamontology.org/topic_3679", "term": "Animal study" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0194", "term": "Phylogenomics" } ], "operatingSystem": [ "Linux" ], "language": [ "PHP", "JavaScript", "Python" ], "license": "GPL-3.0", "collectionID": [ "elixir-fr-sdp-2019" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Data", "Interoperability" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://www.aniseed.fr", "type": [ "Service" ], "note": null }, { "url": "https://twitter.com/Aniseed_DB", "type": [ "Social media" ], "note": "Twitter for ANISEED" }, { "url": "https://www.facebook.com/TunicateCommunity", "type": [ "Social media" ], "note": "Facebook for ANISEED" }, { "url": "https://morphonet.org/", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://www.aniseed.fr/aniseed/download/download_data", "type": "Biological data", "note": null, "version": "2019" } ], "documentation": [ { "url": "https://www.aniseed.fr/api", "type": [ "API documentation" ], "note": null }, { "url": "https://www.aniseed.fr/aniseed/default/privacyPolicy", "type": [ "Contributions policy" ], "note": null }, { "url": "https://www.aniseed.fr/aniseed/default/termOfUse", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkx1108", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "2017", "note": null, "metadata": { "title": "ANISEED 2017: Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets", "abstract": "ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.", "date": "2018-01-01T00:00:00Z", "citationCount": 62, "authors": [ { "name": "Brozovic M." }, { "name": "Dantec C." }, { "name": "Dardaillon J." }, { "name": "Dauga D." }, { "name": "Faure E." }, { "name": "Gineste M." }, { "name": "Louis A." }, { "name": "Naville M." }, { "name": "Nitta K.R." }, { "name": "Piette J." }, { "name": "Reeves W." }, { "name": "Scornavacca C." }, { "name": "Simion P." }, { "name": "Vincentelli R." }, { "name": "Bellec M." }, { "name": "Aicha S.B." }, { "name": "Fagotto M." }, { "name": "Gueroult-Bellone M." }, { "name": "Haeussler M." }, { "name": "Jacox E." }, { "name": "Lowe E.K." }, { "name": "Mendez M." }, { "name": "Roberge A." }, { "name": "Stolfi A." }, { "name": "Yokomori R." }, { "name": "Brown C.T." }, { "name": "Cambillau C." }, { "name": "Christiaen L." }, { "name": "Delsuc F." }, { "name": "Douzery E." }, { "name": "Dumollard R." }, { "name": "Kusakabe T." }, { "name": "Nakai K." }, { "name": "Nishida H." }, { "name": "Satou Y." }, { "name": "Swalla B." }, { "name": "Veeman M." }, { "name": "Volff J.-N." }, { "name": "Lemaire P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkv966", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "2015", "note": null, "metadata": { "title": "ANISEED 2015: A digital framework for the comparative developmental biology of ascidians", "abstract": "Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalisembryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalisgenome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.", "date": "2016-01-01T00:00:00Z", "citationCount": 53, "authors": [ { "name": "Brozovic M." }, { "name": "Martin C." }, { "name": "Dantec C." }, { "name": "Dauga D." }, { "name": "Mendez M." }, { "name": "Simion P." }, { "name": "Percher M." }, { "name": "Laporte B." }, { "name": "Scornavacca C." }, { "name": "Di Gregorio A." }, { "name": "Fujiwara S." }, { "name": "Gineste M." }, { "name": "Lowe E.K." }, { "name": "Piette J." }, { "name": "Racioppi C." }, { "name": "Ristoratore F." }, { "name": "Sasakura Y." }, { "name": "Takatori N." }, { "name": "Brown T.C." }, { "name": "Delsuc F." }, { "name": "Douzery E." }, { "name": "Gissi C." }, { "name": "McDougall A." }, { "name": "Nishida H." }, { "name": "Sawada H." }, { "name": "Swalla B.J." }, { "name": "Yasuo H." }, { "name": "Lemaire P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1101/gr.108175.110", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "2010", "note": null, "metadata": { "title": "The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program", "abstract": "Developmental biology aims to understand how the dynamics of embryonic shapes and organ functions are encoded in linear DNA molecules. Thanks to recent progress in genomics and imaging technologies, systemic approaches are now used in parallel with small-scale studies to establish links between genomic information and phenotypes, often described at the subcellular level. Current model organism databases, however, do not integrate heterogeneous data sets at different scales into a global view of the developmental program. Here, we present a novel, generic digital system, NISEED, and its implementation, ANISEED, to ascidians, which are invertebrate chordates suitable for developmental systems biology approaches. ANISEED hosts an unprecedented combination of anatomical and molecular data on ascidian development. This includes the first detailed anatomical ontologies for these embryos, and quantitative geometrical descriptions of developing cells obtained from reconstructed three-dimensional (3D) embryos up to the gastrula stages. Fully annotated gene model sets are linked to 30,000 high-resolution spatial gene expression patterns in wild-type and experimentally manipulated conditions and to 528 experimentally validated cis-regulatory regions imported from specialized databases or extracted from 160 literature articles. This highly structured data set can be explored via a Developmental Browser, a Genome Browser, and a 3D Virtual Embryo module. We show how integration of heterogeneous data in ANISEED can provide a system-level understanding of the developmental program through the automatic inference of gene regulatory interactions, the identification of inducing signals, and the discovery and explanation of novel asymmetric divisions. © 2010 by Cold Spring Harbor Laboratory Press.", "date": "2010-01-01T00:00:00Z", "citationCount": 90, "authors": [ { "name": "Tassy O." }, { "name": "Dauga D." }, { "name": "Daian F." }, { "name": "Sobral D." }, { "name": "Robin F." }, { "name": "Khoueiry P." }, { "name": "Salgado D." }, { "name": "Fox V." }, { "name": "Caillol D." }, { "name": "Schiappa R." }, { "name": "Laporte B." }, { "name": "Rios A." }, { "name": "Luxardi G." }, { "name": "Kusakabe T." }, { "name": "Joly J.-S." }, { "name": "Darras S." }, { "name": "Christiaen L." }, { "name": "Contensin M." }, { "name": "Auger H." }, { "name": "Lamy C." }, { "name": "Hudson C." }, { "name": "Rothbacher U." }, { "name": "Gilchrist M.J." }, { "name": "Makabe K.W." }, { "name": "Hotta K." }, { "name": "Fujiwara S." }, { "name": "Satoh N." }, { "name": "Satou Y." }, { "name": "Lemaire P." } ], "journal": "Genome Research" } }, { "doi": "10.1016/j.cub.2005.12.044", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "2006", "note": null, "metadata": { "title": "A quantitative approach to the study of cell shapes and interactions during early chordate embryogenesis", "abstract": "Background: The prospects of deciphering the genetic program underlying embryonic development were recently boosted by the generation of large sets of precisely organized quantitative molecular data. In contrast, although the precise arrangement, interactions, and shapes of cells are crucial for the fulfilment of this program, their description remains coarse and qualitative. To bridge this gap, we developed a generic software, 3D Virtual Embryo, to quantify the geometry and interactions of cells in interactive three-dimensional embryo models. We applied this approach to early ascidian embryos, chosen because of their simplicity and their phylogenetic proximity to vertebrates. Results: We generated a collection of 19 interactive ascidian embryos between the 2- and 44-cell stages. We characterized the evolution with time, and in different cell lineages, of the volume of cells and of eight mathematical descriptors of their geometry, and we measured the surface of contact between neighboring blastomeres. These analyses first revealed that early embryonic blastomeres adopt a surprising variety of shapes, which appeared to be under strict and dynamic developmental control. Second, we found novel asymmetric cell divisions in the posterior vegetal lineages, which gave birth to sister cells with different fates. Third, during neural induction, differences in the area of contact between individual competent animal cells and inducing vegetal blastomeres appeared important to select the induced cells. Conclusions: In addition to novel insight into both cell-autonomous and inductive processes controlling early ascidian development, we establish a generic conceptual framework for the quantitative analysis of embryo geometry that can be applied to other model organisms. ©2006 Elsevier Ltd All rights reserved.", "date": "2006-02-21T00:00:00Z", "citationCount": 116, "authors": [ { "name": "Tassy O." }, { "name": "Daian F." }, { "name": "Hudson C." }, { "name": "Bertrand V." }, { "name": "Lemaire P." } ], "journal": "Current Biology" } }, { "doi": "10.1093/nar/gkz955", "pmid": null, "pmcid": null, "type": [], "version": "2019", "note": null, "metadata": { "title": "ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates", "abstract": "ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.", "date": "2020-01-01T00:00:00Z", "citationCount": 31, "authors": [ { "name": "Dardaillon J." }, { "name": "Dauga D." }, { "name": "Simion P." }, { "name": "Faure E." }, { "name": "Onuma T.A." }, { "name": "Debiasse M.B." }, { "name": "Louis A." }, { "name": "Nitta K.R." }, { "name": "Naville M." }, { "name": "Besnardeau L." }, { "name": "Reeves W." }, { "name": "Wang K." }, { "name": "Fagotto M." }, { "name": "Gueroult-Bellone M." }, { "name": "Fujiwara S." }, { "name": "Dumollard R." }, { "name": "Veeman M." }, { "name": "Volff J.-N." }, { "name": "Roest Crollius H." }, { "name": "Douzery E." }, { "name": "Ryan J.F." }, { "name": "Davidson B." }, { "name": "Nishida H." }, { "name": "Dantec C." }, { "name": "Lemaire P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkz955", "pmid": null, "pmcid": null, "type": [], "version": "2019", "note": null, "metadata": null } ], "credit": [ { "name": "Patrick Lemaire", "email": "patrick.lemaire@crbm.cnrs.fr", "url": "http://www.crbm.cnrs.fr/en/team/lemaire/", "orcidid": "https://orcid.org/0000-0003-4925-2009", "gridid": null, "rorid": "01xpc6869", "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Christelle Dantec", "email": "christelle.dantec@crbm.cnrs.fr", "url": "http://www.crbm.cnrs.fr/en/team/lemaire/", "orcidid": "https://orcid.org/0000-0001-7247-6460", "gridid": null, "rorid": "01xpc6869", "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": null, "email": "contact@aniseed.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null } ], "community": null, "owner": "cdantec", "additionDate": "2019-10-19T13:23:03Z", "lastUpdate": "2023-09-25T14:25:18.910230Z", "editPermission": { "type": "group", "authors": [ "delphinedauga" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MorphoNet", "description": "MorphoNet is an interactive morphodynamic web browser designed to help scientists, teachers and students share, analyze and visualize the large 3D morphological datasets that can be generated by modern imaging technology, ranging from live light sheet microscopy of cells and embryos to X Ray tomography of fossils.", "homepage": "https://morphonet.org", "biotoolsID": "morphonet", "biotoolsCURIE": "biotools:morphonet", "version": [ "2.1.3-35b3182" ], "otherID": [], "relation": [ { "biotoolsID": "aniseed", "type": "usedBy" }, { "biotoolsID": "aniseed", "type": "uses" }, { "biotoolsID": "ciona_robusta_anatomy_and_development_ontology", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal", "Desktop application", "Web application", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3064", "term": "Developmental biology" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://morphonet.org/help", "type": [ "Helpdesk", "Helpdesk" ], "note": null }, { "url": "https://www.aniseed.fr", "type": [ "Service" ], "note": null }, { "url": "https://twitter.com/MorphoTweet", "type": [ "Social media" ], "note": null } ], "download": [ { "url": "https://morphonet.org/downloads", "type": "Downloads page", "note": null, "version": null }, { "url": "https://morphonet.org/helpfiles/API/index.html", "type": "API specification", "note": null, "version": null } ], "documentation": [ { "url": "https://morphonet.org/help", "type": [ "General" ], "note": null }, { "url": "https://forum.image.sc/", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1038/s41467-019-10668-1", "pmid": null, "pmcid": "PMC6597584", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MorphoNet: an interactive online morphological browser to explore complex multi-scale data", "abstract": "Powerful novel imaging and image-processing methods are revolutionizing many fields of biology, at scales ranging from the molecule to the functional organ. To support this big-data revolution, we develop a concept of generic web-based morphodynamic browser to interactively visualize complex image datasets, with applications in research and education. MorphoNet handles a broad range of natural or simulated morphological data, onto which quantitative geometric or genetic data can be projected.", "date": "2019-12-01T00:00:00Z", "citationCount": 26, "authors": [ { "name": "Leggio B." }, { "name": "Laussu J." }, { "name": "Carlier A." }, { "name": "Godin C." }, { "name": "Lemaire P." }, { "name": "Faure E." } ], "journal": "Nature Communications" } }, { "doi": "10.1093/nar/gkz955", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates", "abstract": "ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.", "date": "2020-01-01T00:00:00Z", "citationCount": 31, "authors": [ { "name": "Dardaillon J." }, { "name": "Dauga D." }, { "name": "Simion P." }, { "name": "Faure E." }, { "name": "Onuma T.A." }, { "name": "Debiasse M.B." }, { "name": "Louis A." }, { "name": "Nitta K.R." }, { "name": "Naville M." }, { "name": "Besnardeau L." }, { "name": "Reeves W." }, { "name": "Wang K." }, { "name": "Fagotto M." }, { "name": "Gueroult-Bellone M." }, { "name": "Fujiwara S." }, { "name": "Dumollard R." }, { "name": "Veeman M." }, { "name": "Volff J.-N." }, { "name": "Roest Crollius H." }, { "name": "Douzery E." }, { "name": "Ryan J.F." }, { "name": "Davidson B." }, { "name": "Nishida H." }, { "name": "Dantec C." }, { "name": "Lemaire P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Emmanuel FAURE", "email": "emmanuel.faure@lirmm.fr", "url": null, "orcidid": "https://orcid.org/0000-0003-2787-0885", "gridid": null, "rorid": "013yean28", "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "cdantec", "additionDate": "2023-09-25T13:33:15.447513Z", "lastUpdate": "2023-09-25T14:12:08.944886Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ProtVar", "description": "ProtVar helps users to contextualise and evaluate human missense variation at a per-residue level. It can be accessed via genomic coordinates, IDs or protein positions in over 92% of human proteins. Functional and structural annotations, predictions and co-located variants can be explored via an interactive UI or accessed programatically via an API.", "homepage": "https://www.ebi.ac.uk/ProtVar/", "biotoolsID": "protvar", "biotoolsCURIE": "biotools:protvar", "version": [], "otherID": [], "relation": [ { "biotoolsID": "open_targets_platform", "type": "usedBy" }, { "biotoolsID": "uniprot", "type": "uses" }, { "biotoolsID": "uniprot", "type": "usedBy" }, { "biotoolsID": "ensembl", "type": "uses" }, { "biotoolsID": "pdbe", "type": "uses" }, { "biotoolsID": "dbsnp", "type": "uses" }, { "biotoolsID": "clinvar", "type": "uses" }, { "biotoolsID": "crossmap", "type": "uses" }, { "biotoolsID": "alphafold_2", "type": "uses" }, { "biotoolsID": "eve", "type": "uses" }, { "biotoolsID": "cadd_phred", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2520", "term": "DNA mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2887", "term": "Nucleic acid sequence record" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_2187", "term": "UniProt-like (text)" } ] } ], "note": "ProtVar maps missense variants from genomic coordinates to UniProt protein positions in all isoforms.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3661", "term": "SNP annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2887", "term": "Nucleic acid sequence record" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3779", "term": "Annotated text" }, "format": [ { "uri": "http://edamontology.org/format_2187", "term": "UniProt-like (text)" } ] } ], "note": "ProtVar annotates missense variant positions with functional and structural information for the amino acid affected, the protein region and the overall protein role from curated and high throughput sources.", "cmd": null } ], "toolType": [ "Web application", "Web API", "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_2533", "term": "DNA mutation" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java" ], "license": null, "collectionID": [ "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://twitter.com/EBIProtVar", "type": [ "Social media" ], "note": null }, { "url": "https://docs.google.com/forms/d/e/1FAIpQLSd7P85zRHVspesU3kgF3qWpzSDSYFsyeGFmnkuyzB00HNDmDw/viewform?usp=sf_link", "type": [ "Mailing list" ], "note": null } ], "download": [], "documentation": [ { "url": "https://www.ebi.ac.uk/ProtVar/help", "type": [ "User manual" ], "note": "This is a link to the help section in ProtVar with annotated screen shots to help you navigate the tool and understand the data." } ], "publication": [], "credit": [ { "name": "James Stephenson", "email": "jstephenson@ebi.ac.uk", "url": "https://www.ebi.ac.uk/people/person/james-stephenson/", "orcidid": "https://orcid.org/0000-0002-6427-5703", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Maintainer", "Documentor" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": "https://www.ebi.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Prabhat Totoo", "email": null, "url": "https://www.ebi.ac.uk/people/person/prabhat-totoo/", "orcidid": "https://orcid.org/0000-0001-5923-4467", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Open Targets", "email": null, "url": "https://www.opentargets.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null } ], "community": null, "owner": "JStephenson", "additionDate": "2023-09-21T09:05:33.125111Z", "lastUpdate": "2023-09-25T09:31:39.599149Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RNAct", "description": "Protein–RNA interaction predictions for model organisms\nwith supporting experimental data, enabling a global view of the protein–RNA interactome. RNAct currently covers the human, mouse and yeast genomes and contains a total of 5.87 billion pairwise interactions, reflecting nearly 120 years of computation time on the CRG's high-performance computing cluster. It combines experimentally identified interactions (e.g. from ENCODE) with ab initio predictions, enabling full coverage of the RNA-binding proteome.", "homepage": "https://rnact.tartaglialab.com", "biotoolsID": "RNAct", "biotoolsCURIE": "biotools:RNAct", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1026", "term": "Gene symbol" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1033", "term": "Ensembl gene ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2725", "term": "Ensembl transcript ID" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": "Retrieve protein–RNA interaction data, including genome-wide pre-calculated prediction scores for human, mouse, and yeast, as well as experimentally determined interaction data from the ENCODE Project.", "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_0099", "term": "RNA" } ], "operatingSystem": [], "language": [], "license": "CC-BY-NC-SA-4.0", "collectionID": [ "RNAct" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://rnact.crg.eu/download", "type": "Biological data", "note": "Download genome-wide protein-RNA interaction predictions.\n\nThese tab-separated interactome files contain our genome-wide catRAPID interaction prediction scores, as described in the About section (http://rnact.crg.eu/about).\n\nThe Supporting Tables contain protein and RNA annotation, identifier mappings used internally for searching, and particularly the experimental data from the ENCODE Project which is available in RNAct.", "version": null } ], "documentation": [ { "url": "https://rnact.tartaglialab.com/about", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gky967", "pmid": "30445601", "pmcid": "PMC6324028", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data", "abstract": "Protein-RNA interactions are implicated in a number of physiological roles as well as diseases, with molecular mechanisms ranging from defects in RNA splicing, localization and translation to the formation of aggregates. Currently, ∼1400 human proteins have experimental evidence of RNA-binding activity. However, only ∼250 of these proteins currently have experimental data on their target RNAs from various sequencing-based methods such as eCLIP. To bridge this gap, we used an established, computationally expensive protein-RNA interaction prediction method, catRAPID, to populate a large database, RNAct. RNAct allows easy lookup of known and predicted interactions and enables global views of the human, mouse and yeast protein-RNA interactomes, expanding them in a genome-wide manner far beyond experimental data (http://rnact.crg.eu).", "date": "2019-01-08T00:00:00Z", "citationCount": 54, "authors": [ { "name": "Lang B." }, { "name": "Armaos A." }, { "name": "Tartaglia G.G." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Benjamin Lang", "email": "benjamin.lang@crg.eu", "url": "https://www.crg.eu/en/group-members/benjamin-lang", "orcidid": "http://orcid.org/0000-0001-6358-8380", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": "Marie Sklodowska-Curie Postdoctoral Fellow (MSCA-IF), Gene Function and Evolution (Dr. Gian Tartaglia), Centre for Genomic Regulation (CRG), Barcelona, Spain" }, { "name": "Alexandros Armaos", "email": "alexandros.armaos@crg.eu", "url": "https://www.crg.eu/ca/group-members/alexandros-armaos", "orcidid": "https://orcid.org/0000-0003-0607-5663", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "PhD Student, Gene Function and Evolution (Dr. Gian Tartaglia), Centre for Genomic Regulation (CRG), Barcelona, Spain" }, { "name": "Gian Gaetano Tartaglia", "email": "gian@tartaglialab.com", "url": "http://www.tartaglialab.com", "orcidid": "https://orcid.org/0000-0001-7524-6310", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "ICREA Research Professor & Junior Group Leader, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain" } ], "community": null, "owner": "blang", "additionDate": "2019-03-20T16:23:17Z", "lastUpdate": "2023-09-21T15:02:34.671872Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "VAMB", "description": "Improved metagenome binning and assembly using deep variational autoencoders.\n\nVamb is a metagenomic binner which feeds sequence composition information from a contig catalogue and co-abundance information from BAM files into a variational autoencoder and clusters the latent representation.", "homepage": "https://github.com/RasmussenLab/vamb", "biotoolsID": "vamb", "biotoolsCURIE": "biotools:vamb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3432", "term": "Clustering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] }, { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_0605", "term": "Informatics" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://figshare.com/projects/VAMB/72677", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/S41587-020-00777-4", "pmid": "33398153", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Improved metagenome binning and assembly using deep variational autoencoders", "abstract": "Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that uses deep variational autoencoders to encode sequence coabundance and k-mer distribution information before clustering. We show that a variational autoencoder is able to integrate these two distinct data types without any previous knowledge of the datasets. VAMB outperforms existing state-of-the-art binners, reconstructing 29–98% and 45% more near-complete (NC) genomes on simulated and real data, respectively. Furthermore, VAMB is able to separate closely related strains up to 99.5% average nucleotide identity (ANI), and reconstructed 255 and 91 NC Bacteroides vulgatus and Bacteroides dorei sample-specific genomes as two distinct clusters from a dataset of 1,000 human gut microbiome samples. We use 2,606 NC bins from this dataset to show that species of the human gut microbiome have different geographical distribution patterns. VAMB can be run on standard hardware and is freely available at https://github.com/RasmussenLab/vamb.", "date": "2021-05-01T00:00:00Z", "citationCount": 103, "authors": [ { "name": "Nissen J.N." }, { "name": "Johansen J." }, { "name": "Allesoe R.L." }, { "name": "Sonderby C.K." }, { "name": "Armenteros J.J.A." }, { "name": "Gronbech C.H." }, { "name": "Jensen L.J." }, { "name": "Nielsen H.B." }, { "name": "Petersen T.N." }, { "name": "Winther O." }, { "name": "Rasmussen S." } ], "journal": "Nature Biotechnology" } } ], "credit": [ { "name": "Simon Rasmussen", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "jakobnissen", "additionDate": "2021-03-19T08:31:09Z", "lastUpdate": "2023-09-07T14:22:51.550298Z", "editPermission": { "type": "group", "authors": [ "jakobnissen" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ChIP-Seq", "description": "The ChIP-seq web server provides access to a set of useful tools performing common ChIP-seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. It is an open system designed to allow interoperability with other resources, in particular the motif discovery programs from the Signal Search Analysis (SSA) server.", "homepage": "https://epd.expasy.org/chipseq/", "biotoolsID": "chip-seq", "biotoolsCURIE": "biotools:chip-seq", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3222", "term": "Peak calling" }, { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_3169", "term": "ChIP-seq" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl", "C" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://epd.expasy.org/chipseq/tutorials.php", "type": [ "User manual" ], "note": null }, { "url": "https://epd.expasy.org/chipseq/general_doc.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s12864-016-3288-8", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The ChIP-Seq tools and web server: A resource for analyzing ChIP-seq and other types of genomic data", "abstract": "Background: ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data. Results: Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade. Conclusions: The various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools. The ChIP-Seq server is accessible at http://ccg.vital-it.ch/chipseq/.", "date": "2016-11-18T00:00:00Z", "citationCount": 16, "authors": [ { "name": "Ambrosini G." }, { "name": "Dreos R." }, { "name": "Kumar S." }, { "name": "Bucher P." } ], "journal": "BMC Genomics" } } ], "credit": [ { "name": "SIB Swiss Institute of Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "EPD", "email": "epd@sib.swiss", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "sduvaud", "additionDate": "2017-01-13T13:13:59Z", "lastUpdate": "2023-09-05T10:33:10.520352Z", "editPermission": { "type": "group", "authors": [ "metanetx" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SSA", "description": "SSA (Signal Search Analysis) is a software package for the analysis of nucleic acid sequence motifs that are postionally correlated with a functional site (e.g a transcription or translation initiation site).", "homepage": "https://epd.expasy.org/ssa/", "biotoolsID": "ssa", "biotoolsCURIE": "biotools:ssa", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_0238", "term": "Sequence motif discovery" }, { "uri": "http://edamontology.org/operation_0240", "term": "Sequence motif comparison" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl", "Fortran", "C" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://epd.expasy.org/ssa/doc/ssa_tutorial.php", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": null, "pmid": "12824379", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Signal search analysis server", "abstract": "Signal search analysis is a general method to discover and characterize sequence motifs that are positionally correlated with a functional site (e.g. a transcription or translation start site). The method has played an instrumental role in the analysis of eukaryotic promoter elements. The signal search analysis server provides access to four different computer programs as well as to a large number of precompiled functional site collections. The programs offered allow: (i) the identification of non-random sequence regions under evolutionary constraint; (ii) the detection of consensus sequence-based motifs that are over- or under-represented at a particular distance from a functional site; (iii) the analysis of the positional distribution of a consensus sequence- or weight matrix-based sequence motif around a functional site; and (iv) the optimization of a weight matrix description of a locally over-represented sequence motif. These programs can be accessed at: http://www.isrec.isb-sib.ch/ssa/.", "date": "2003-07-01T00:00:00Z", "citationCount": 20, "authors": [ { "name": "Ambrosini G." }, { "name": "Praz V." }, { "name": "Jagannathan V." }, { "name": "Bucher P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "SIB Swiss Institute of Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "Prof. Philipp Bucher", "email": "epd@sib.swiss", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "sduvaud", "additionDate": "2017-01-13T13:16:40Z", "lastUpdate": "2023-09-05T10:29:08.667997Z", "editPermission": { "type": "group", "authors": [ "metanetx" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ARTEM", "description": "ARTEM is a tool for the superposition of two arbitrary RNA 3D structure fragments.\nARTEM doesn’t rely on sequence similarity, annotated interactions, or backbone topology. Instead, ARTEM assumes at least one residue-residue match has a close-to-zero RMSD in the ideal superposition. Then, ARTEM tries all N*M single-residue matches and derives a subset of mutually closest residues as the matches for each of the single-residue-based superpositions. Finally, ARTEM returns the superpositions ordered by their size, letting the user choose the best one based on any specific requirements. ARTEM can read/write both PDB and mmCIF format.", "homepage": "https://github.com/david-bogdan-r/ARTEM", "biotoolsID": "artem", "biotoolsCURIE": "biotools:artem", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0509", "term": "Local structure alignment" }, { "uri": "http://edamontology.org/operation_0503", "term": "Pairwise structure alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1465", "term": "RNA structure" }, "format": [ { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1493", "term": "RNA structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": null, "cmd": "python3 artem.py r=FILENAME q=FILENAME [OPTIONS]" } ], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" }, { "uri": "http://edamontology.org/topic_0099", "term": "RNA" }, { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/david-bogdan-r/ARTEM", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://doi.org/10.5281/zenodo.8009615", "type": "Software package", "note": null, "version": "ver1.0" } ], "documentation": [ { "url": "https://github.com/david-bogdan-r/ARTEM/blob/main/README.md", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkad605", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Davyd Bohdan", "email": "bogdan.d@phystech.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-6456-6658", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null } ], "community": null, "owner": "febos", "additionDate": "2023-09-04T12:19:37.685404Z", "lastUpdate": "2023-09-04T12:31:24.146202Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MS Annika", "description": "MS Annika is a cross-linking search engine for use with cleavable cross-linkers and MS2 or MS2-MS3 spectra. It can deal with a wide variety of cleavable cross-linkers and provides robust and transparent FDR control based on a target-decoy approach. MS Annika is available free of charge as a plug-in for Proteome Discoverer.", "homepage": "https://ms.imp.ac.at/?action=ms-annika", "biotoolsID": "ms_annika", "biotoolsCURIE": "biotools:ms_annika", "version": [ "Proteome Discoverer 3.1: MS Annika 2.0 v1.2.0", "Proteome Discoverer 3.0: MS Annika 2.0 v1.1.4", "Proteome Discoverer 2.5: MS Annika 2.0 v1.1.3", "Proteome Discoverer 2.4: MS Annika v1.0.0", "Proteome Discoverer 2.3: MS Annika v1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3631", "term": "Peptide identification" }, { "uri": "http://edamontology.org/operation_3646", "term": "Peptide database search" }, { "uri": "http://edamontology.org/operation_3645", "term": "PTM identification" }, { "uri": "http://edamontology.org/operation_3755", "term": "PTM localisation" }, { "uri": "http://edamontology.org/operation_3649", "term": "Target-Decoy" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3712", "term": "Thermo RAW" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Windows" ], "language": [ "C#" ], "license": "Freeware", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/hgb-bin-proteomics/MSAnnika", "type": [ "Repository" ], "note": "MS Annika version archive" }, { "url": "https://github.com/hgb-bin-proteomics/MSAnnika_exporters", "type": [ "Repository" ], "note": "MS Annika export tools" }, { "url": "https://github.com/hgb-bin-proteomics/MSAnnika_CSM_Annotation", "type": [ "Repository" ], "note": "MS Annika annotation tools" } ], "download": [ { "url": "https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.1/latest.zip", "type": "Software package", "note": "Latest MS Annika version for Proteome Disoverer 3.1", "version": "PD3.1:latest" }, { "url": "https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.0/latest.zip", "type": "Software package", "note": "Latest MS Annika version for Proteome Disoverer 3.0", "version": "PD3.0:latest" }, { "url": "https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD2.5/latest.zip", "type": "Software package", "note": "Latest MS Annika version for Proteome Disoverer 2.5", "version": "PD2.5:latest" } ], "documentation": [ { "url": "https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/MS_Annika_UserManual.pdf", "type": [ "User manual" ], "note": null }, { "url": "https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/tutorial/MS_Annika_2.0_Tutorial.pdf", "type": [ "Training material" ], "note": "Detailed tutorial how to use MS Annika 2.0" }, { "url": "https://www.youtube.com/watch?v=L1lVt35PYv4", "type": [ "Training material" ], "note": "Detailed tutorial how to use MS Annika 2.0" } ], "publication": [ { "doi": "10.1021/acs.jproteome.0c01000", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "MS Annika for cleavable crosslink identification from MS2 spectra", "metadata": { "title": "MS Annika: A New Cross-Linking Search Engine", "abstract": "Cross-linking mass spectrometry (XL-MS) has become a powerful technique that enables insights into protein structures and protein interactions. The development of cleavable cross-linkers has further promoted XL-MS through search space reduction, thereby allowing for proteome-wide studies. These new analysis possibilities foster the development of new cross-linkers, which not every search engine can deal with out of the box. In addition, some search engines for XL-MS data also struggle with the validation of identified cross-linked peptides, that is, false discovery rate (FDR) estimation, as FDR calculation is hampered by the fact that not only one but two peptides in a single spectrum have to be correct. We here present our new search engine, MS Annika, which can identify cross-linked peptides in MS2 spectra from a wide variety of cleavable cross-linkers. We show that MS Annika provides realistic estimates of FDRs without the need of arbitrary score cutoffs, being able to provide on average 44% more identifications at a similar or better true FDR than comparable tools. In addition, MS Annika can be used on proteome-wide studies due to fast, parallelized processing and provides a way to visualize the identified cross-links in protein 3D structures.", "date": "2021-05-07T00:00:00Z", "citationCount": 16, "authors": [ { "name": "Pirklbauer G.J." }, { "name": "Stieger C.E." }, { "name": "Matzinger M." }, { "name": "Winkler S." }, { "name": "Mechtler K." }, { "name": "Dorfer V." } ], "journal": "Journal of Proteome Research" } }, { "doi": "10.1021/acs.jproteome.3c00325", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "MS Annika 2.0 for cleavable crosslink identification from MS3 spectra", "metadata": { "title": "MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity", "abstract": "Cross-linking mass spectrometry has become a powerful tool for the identification of protein-protein interactions and for gaining insight into the structures of proteins. We previously published MS Annika, a cross-linking search engine which can accurately identify cross-linked peptides in MS2 spectra from a variety of different MS-cleavable cross-linkers. In this publication, we present MS Annika 2.0, an updated version implementing a new search algorithm that, in addition to MS2 level, only supports the processing of data from MS2-MS3-based approaches for the identification of peptides from MS3 spectra, and introduces a novel scoring function for peptides identified across multiple MS stages. Detected cross-links are validated by estimating the false discovery rate (FDR) using a target-decoy approach. We evaluated the MS3-search-capabilities of MS Annika 2.0 on five different datasets covering a variety of experimental approaches and compared it to XlinkX and MaXLinker, two other cross-linking search engines. We show that MS Annika detects up to 4 times more true unique cross-links while simultaneously yielding less false positive hits and therefore a more accurate FDR estimation than the other two search engines. All mass spectrometry proteomics data along with result files have been deposited to the ProteomeXchange consortium via the PRIDE partner repository with the dataset identifier PXD041955.", "date": "2023-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Birklbauer M.J." }, { "name": "Matzinger M." }, { "name": "Muller F." }, { "name": "Mechtler K." }, { "name": "Dorfer V." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "Viktoria Dorfer", "email": "viktoria.dorfer@fh-hagenberg.at", "url": "http://bioinformatics.fh-hagenberg.at/", "orcidid": "https://orcid.org/0000-0002-5332-5701", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Micha Birklbauer", "email": "micha.birklbauer@fh-hagenberg.at", "url": "http://bioinformatics.fh-hagenberg.at/", "orcidid": "https://orcid.org/0009-0005-1051-179X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "community": null, "owner": "michabirklbauer", "additionDate": "2023-07-26T14:40:01.768324Z", "lastUpdate": "2023-09-04T11:15:23.174692Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Classical Molecular Interaction Potentials (CMIP)", "description": "CMIP performs a series of analysis centered in the obtention of molecular interaction potentials using classic formalisms:\nElectrostatic interactions through coulombic potentials with several dielectric options or Poisson-Boltzmann equation\nVan de Waals potentials computed from the Lennard-Jones expression\nElectrostatic Solvation energy evaluated from PB potentials\nHydrophobic Solvation from surface analysis with a variety of alternative scales.", "homepage": "https://mmb.irbbarcelona.org/gitlab/gelpi/CMIP", "biotoolsID": "classical_molecular_interaction_potentials_cmip", "biotoolsCURIE": "biotools:classical_molecular_interaction_potentials_cmip", "version": [ "2.6.1" ], "otherID": [], "relation": [ { "biotoolsID": "biobb", "type": "includedIn" }, { "biotoolsID": "bioexcel_building_blocks_tutorials_molecular_interaction_potentials", "type": "includedIn" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0250", "term": "Protein property calculation" }, { "uri": "http://edamontology.org/operation_0248", "term": "Residue interaction calculation" }, { "uri": "http://edamontology.org/operation_0272", "term": "Residue contact prediction" } ], "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_0906", "term": "Protein interaction data" }, "format": [ { "uri": "http://edamontology.org/format_1637", "term": "dat" }, { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "Fortran" ], "license": "Apache-2.0", "collectionID": [ "BioExcel", "BSC" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Interoperability" ], "elixirNode": [ "Spain" ], "elixirCommunity": [], "link": [ { "url": "https://mmb.irbbarcelona.org/gitlab/gelpi/CMIP", "type": [ "Repository" ], "note": "Source Code in GitLab" } ], "download": [ { "url": "https://anaconda.org/bioconda/cmip", "type": "Software package", "note": "BioConda package", "version": null }, { "url": "https://mmb.irbbarcelona.org/gitlab/gelpi/CMIP", "type": "Source code", "note": "Source Code in GitLab", "version": null } ], "documentation": [ { "url": "https://mmb.irbbarcelona.org/gitlab/gelpi/CMIP/-/blob/master/CMIP.man", "type": [ "User manual" ], "note": "CMIP User Manual" } ], "publication": [ { "doi": "10.1002/prot.1159", "pmid": "11746690", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins", "abstract": "The latest version of the classical molecular interaction potential (CMIP) has the ability to predict the position of crystallographic waters in several proteins with great accuracy. This article analyzes the ability of the CMIP functional to improve the setup procedure of the molecular system in molecular dynamics (MD) simulations of proteins. To this end, the CMIP strategy is used to include both water molecules and counterions in different protein systems. The structural details of the configurations sampled from trajectories obtained using the CMIP setup procedure are compared with those obtained from trajectories derived from a standard equilibration process. The results show that standard MD simulations can lead to artifactual results, which are avoided using the CMIP setup procedure. Because the CMIP is easy to implement at a low computational cost, it can be very useful in obtaining reliable MD trajectories. © 2001 Wiley-Liss, Inc.", "date": "2001-12-01T00:00:00Z", "citationCount": 86, "authors": [ { "name": "Gelpi J.L." }, { "name": "Kalko S.G." }, { "name": "Barril X." }, { "name": "Cirera J." }, { "name": "De La Cruz X." }, { "name": "Luque F.J." }, { "name": "Orozco M." } ], "journal": "Proteins: Structure, Function and Genetics" } } ], "credit": [ { "name": "Josep Lluís Gelpí", "email": "gelpi@ub.edu", "url": "https://www.bsc.es/es/gelpi-josep", "orcidid": "https://orcid.org/0000-0002-0566-7723", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer", "Support" ], "note": null } ], "community": null, "owner": "adam.hospital@irbbarcelona.org", "additionDate": "2023-08-31T07:29:49.062944Z", "lastUpdate": "2023-08-31T07:30:28.315262Z", "editPermission": { "type": "group", "authors": [ "gelpi@ub.edu" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }