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{ "count": 2017, "next": "?page=2", "previous": null, "list": [ { "name": "GENtle", "description": "Software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more.", "homepage": "http://gentle.magnusmanske.de/", "biotoolsID": "gentle", "biotoolsCURIE": "biotools:gentle", "version": [ "1.9.4" ], "otherID": [], "relation": [], "function": [], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_3912", "term": "Genetic engineering" }, { "uri": "http://edamontology.org/topic_3519", "term": "PCR experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "C++" ], "license": "GPL-2.0", "collectionID": [], "maturity": "Legacy", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/GENtle-persons/gentle-m", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/GENtle-persons/gentle-m/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "https://en.wikibooks.org/wiki/GENtle", "type": [ "User manual" ], "note": null } ], "publication": [], "credit": [], "community": null, "owner": "smoe", "additionDate": "2023-09-02T07:29:28.160089Z", "lastUpdate": "2023-09-02T07:39:00.374787Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "pyM2aia", "description": "pyM²aia is a Python package for memory-efficient access and processing of mass spectrometry image data. The I/O functionality is derived from the interactive desktop application M²aia. Special features are the batch generator utilities for deep learning applications.", "homepage": "https://m2aia.de/pym2aia.html", "biotoolsID": "pym2aia", "biotoolsCURIE": "biotools:pym2aia", "version": [], "otherID": [], "relation": [ { "biotoolsID": "m2aia", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_3694", "term": "Mass spectrum visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" }, { "uri": "http://edamontology.org/format_3839", "term": "ibd" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "C++" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/m2aia/pym2aia", "type": [ "Issue tracker", "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/m2aia/pym2aia", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://data.jtfc.de/pym2aia/sphinx-build/html/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/gigascience/giab049", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "Cordes J; Enzlein T; Marsching C; Hinze M; Engelhardt S; Hopf C; Wolf I (July, 2021): M²aia - Interactive, fast and memory efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data https://doi.org/10.1093/gigascience/giab049", "metadata": null } ], "credit": [ { "name": "Jonas Cordes", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3148-4282", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "jannikwitte", "additionDate": "2023-08-30T09:06:30.320364Z", "lastUpdate": "2023-08-30T09:09:08.519629Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CarveMe", "description": "CarveMe is a python-based automated tool used for top-down genome-scale metabolic model reconstruction. It can predict an organism's uptake and secretion capabilities without requiring gap-filling, although gap-filling is also supported. Additionally, CarveMe allows the generation of microbial community models by merging single species models. The tool offers advanced features such as manual adjustment of blasting options, an orthology-based search using eggNOG-mapper (kegg-bigg branch), the ability to provide a custom media library for gap-filling, and the generation of models compatible with various SBML formats. Furthermore, CarveMe supports ensemble modeling, which helps explore how different alternative solutions can lead to diverse network structures and predict various phenotypes. During the model carving process, users can select from provided templates or create their own customized universe model to suit their specific needs.", "homepage": "https://github.com/cdanielmachado/carveme", "biotoolsID": "carveme", "biotoolsCURIE": "biotools:carveme", "version": [ "1.0.0", "1.1.0", "1.2.0", "1.3.0", "1.4.0 - 1.4.1", "1.5.0 - 1.5.2" ], "otherID": [], "relation": [ { "biotoolsID": "bigg_models", "type": "uses" }, { "biotoolsID": "diamond", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3660", "term": "Metabolic network modelling" }, { "uri": "http://edamontology.org/operation_3663", "term": "Homology-based gene prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2787", "term": "NCBI genome accession" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2984", "term": "Pathway or network report" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_2585", "term": "SBML" } ] } ], "note": "Homology-based search is default using diamond. Orthology-based search can be performed with eggNOG-mapper (kegg-bigg branch).", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3217", "term": "Scaffold gap completion" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2787", "term": "NCBI genome accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2984", "term": "Pathway or network report" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] }, { "data": { "uri": "http://edamontology.org/data_3724", "term": "Cultivation parameter" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2984", "term": "Pathway or network report" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_2585", "term": "SBML" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2984", "term": "Pathway or network report" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2984", "term": "Pathway or network report" }, "format": [ { "uri": "http://edamontology.org/format_2585", "term": "SBML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3391", "term": "Omics" }, { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "ELIXIR-NO", "ELIXIR-Norway", "NTNU tools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Norway" ], "elixirCommunity": [ "Marine Metagenomics", "Metabolomics", "Microbial Biotechnology", "Proteomics" ], "link": [ { "url": "https://github.com/cdanielmachado/carveme", "type": [ "Repository", "Issue tracker" ], "note": null }, { "url": "https://elixir.no/helpdesk", "type": [ "Helpdesk" ], "note": "Helpdesk and support for ELIXIR Norway services" } ], "download": [ { "url": "https://github.com/cdanielmachado/carveme/releases/tag/1.5.2", "type": "Source code", "note": "Latest release as of 3 August 2023", "version": "1.5.2" }, { "url": "https://github.com/cdanielmachado/carveme/releases", "type": "Source code", "note": null, "version": "All" } ], "documentation": [ { "url": "https://carveme.readthedocs.io/en/latest/index.html", "type": [ "General", "Installation instructions", "Quick start guide", "Command-line options", "User manual" ], "note": null }, { "url": "https://github.com/cdanielmachado/carveme#readme", "type": [ "Citation instructions" ], "note": null }, { "url": "https://github.com/cdanielmachado/carveme/releases", "type": [ "Release notes" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gky537", "pmid": "30192979", "pmcid": "PMC6125623", "type": [ "Primary" ], "version": "1.0.0", "note": null, "metadata": { "title": "Fast automated reconstruction of genome-scale metabolic models for microbial species and communities", "abstract": "Genome-scale metabolic models are instrumental in uncovering operating principles of cellular metabolism, for model-guided re-engineering, and unraveling cross-feeding in microbial communities. Yet, the application of genome-scale models, especially to microbial communities, is lagging behind the availability of sequenced genomes. This is largely due to the time-consuming steps of manual curation required to obtain good quality models. Here, we present an automated tool, CarveMe, for reconstruction of species and community level metabolic models. We introduce the concept of a universal model, which is manually curated and simulation ready. Starting with this universal model and annotated genome sequences, CarveMe uses a topdown approach to build single-species and community models in a fast and scalable manner. We show that CarveMe models perform closely to manually curated models in reproducing experimental phenotypes (substrate utilization and gene essentiality). Additionally, we build a collection of 74 models for human gut bacteria and test their ability to reproduce growth on a set of experimentally defined media. Finally, we create a database of 5587 bacterial models and demonstrate its potential for fast generation of microbial community models. Overall, CarveMe provides an open-source and user-friendly tool towards broadening the use of metabolic modeling in studying microbial species and communities.", "date": "2018-09-06T00:00:00Z", "citationCount": 239, "authors": [ { "name": "Machado D." }, { "name": "Andrejev S." }, { "name": "Tramontano M." }, { "name": "Patil K.R." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1038/s41559-022-01939-0", "pmid": "36471121", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Reply to: Erroneous predictions of auxotrophies by CarveMe", "abstract": "", "date": "2023-02-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Machado D." }, { "name": "Patil K.R." } ], "journal": "Nature Ecology and Evolution" } } ], "credit": [ { "name": "Daniel Machado", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-2063-5383", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer" ], "note": null }, { "name": "The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk", "email": "support@elixir.no", "url": "https://elixir.no/helpdesk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Support" ], "note": null }, { "name": "Sergej Andrejev", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-7875-0261", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Melanie Tramontano", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-6407-527X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Kiran Raosaheb Patil", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6166-8640", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "NTNU", "email": null, "url": "http://www.ntnu.edu", "orcidid": null, "gridid": "grid.5947.f", "rorid": "05xg72x27", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": "Developed at NTNU 2020-present" }, { "name": "European Molecular Biology Laboratory (EMBL)", "email": null, "url": "http://embl.org/", "orcidid": null, "gridid": "grid.4709.a", "rorid": "03mstc592", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": "Developed at EMBL 2017-2019" }, { "name": "European Union's Horizon 2020", "email": null, "url": "https://doi.org/10.3030/686070", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "Erin Calhoun", "email": "erin.calhoun@uit.no", "url": null, "orcidid": "https://orcid.org/0009-0003-3752-7156", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": "Curation of bio.tools profile - contact me with updates/corrections." } ], "community": null, "owner": "dmachado", "additionDate": "2021-02-18T12:08:51Z", "lastUpdate": "2023-08-15T10:51:32.592010Z", "editPermission": { "type": "group", "authors": [ "eca008" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "omnipy", "description": "Omnipy is a Python library for type-driven data wrangling and scalable data flow orchestration. It simplifies creation and deployment of (meta)data transformation processes, emphasizing FAIRification, executable metadata crosswalks and data brokering. Omnipy aids generic data tasks like extraction from multiple sources, (meta)data mapping and systematic data model transformations. Embracing a \"parse, don't validate\" approach, omnipy uses Python type hints and pydantic for data consistency and adherence to specific models. Highly modular, it allows integration of (meta)data transformation steps dependent on software like pandas and R. The architecture supports pluggable execution engines like Prefect, a highly interoperable industry-developed Open Source data flow orchestration engine. Envisioned as a community effort, omnipy aims to offer various import formats and data models (both hierarchical and tabular representations), as well as ontology mapping and semiautomatic data cleaning.", "homepage": "https://fairtracks.net/fair/#fair-07-transformation", "biotoolsID": "omnipy", "biotoolsCURIE": "biotools:omnipy", "version": [ "0.10.4" ], "otherID": [], "relation": [ { "biotoolsID": "pandas", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3763", "term": "Service invocation" }, { "uri": "http://edamontology.org/operation_2429", "term": "Mapping" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2093", "term": "Data reference" }, "format": [ { "uri": "http://edamontology.org/format_3996", "term": "Python script" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "note": "Import diverse data from API endpoints (JSON) and relational databases. Output as JSON files specifying fields from the mapping API or as pandas DataFrames with reference metadata.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3357", "term": "Format detection" }, { "uri": "http://edamontology.org/operation_1812", "term": "Parsing" }, { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" }, { "uri": "http://edamontology.org/operation_3096", "term": "Editing" }, { "uri": "http://edamontology.org/operation_3359", "term": "Splitting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2526", "term": "Text data" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_2333", "term": "Binary format" }, { "uri": "http://edamontology.org/format_3775", "term": "GSuite" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [] } ], "note": "Import data as files in a supported format. Output as pandas DataFrames with embedded JSON objects/lists and reference metadata.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [] } ], "note": "Data cleanup and transformation.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2429", "term": "Mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0954", "term": "Database cross-mapping" }, "format": [] } ], "note": "Manual mapping of FAIRtracks objects and attributes to corresponding tables and columns in the original data.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_2429", "term": "Mapping" }, { "uri": "http://edamontology.org/operation_3763", "term": "Service invocation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2093", "term": "Data reference" }, "format": [ { "uri": "http://edamontology.org/format_3033", "term": "Matrix format" } ] }, { "data": { "uri": "http://edamontology.org/data_0954", "term": "Database cross-mapping" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3509", "term": "Ontology mapping" }, "format": [ { "uri": "http://edamontology.org/format_3033", "term": "Matrix format" } ] } ], "note": "Generate initial FAIRtracks tables by applying the model map, mapping FAIRtracks attributes with one or more attributes (columns) in the original table.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2428", "term": "Validation" }, { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_3345", "term": "Data identity and mapping" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_3473", "term": "Data mining" }, { "uri": "http://edamontology.org/topic_3572", "term": "Data quality management" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" }, { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], 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"elixir_badge": 0, "confidence_flag": null }, { "name": "JASPAR RESTful API", "description": "JASPAR is a widely used open-access database containing curated, non-redundant transcription factor binding profiles. The JASPAR RESTful API enhances accessibility by enabling users to programmatically access the database by most programming languages.The API uses the Representational State Transfer (REST) architecture to provide data in multiple formats (JSON, JSONP, JASPAR, MEME, PFM, TRANSFAC, BED, and YAML). 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Currently, data from JASPAR can be retrieved as flat files or by using programming language-specific interfaces. Here, we present a programming language-independent application programming interface (API) to access JASPAR data using the Representational State Transfer (REST) architecture. The REST API enables programmatic access to JASPAR by most programming languages and returns data in eight widely used formats. Several endpoints are available to access the data and an endpoint is available to infer the TF binding profile(s) likely bound by a given DNA binding domain protein sequence. Additionally, it provides an interactive browsable interface for bioinformatics tool developers. Availability and implementation This REST API is implemented in Python using the Django REST Framework. It is accessible at http://jaspar.genereg.net/api/ and the source code is freely available at https://bitbucket.org/CBGR/jaspar under GPL v3 license. Contact aziz.khan@ncmm.uio.no or anthony.mathelier@ncmm.uio.no Supplementary informationSupplementary dataare available at Bioinformatics online.", "date": "2018-05-01T00:00:00Z", "citationCount": 11, "authors": [ { "name": "Khan A." }, { "name": "Mathelier A." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/nar/gkab1113", "pmid": "34850907", "pmcid": "PMC8728201", "type": [ "Other" ], "version": "1", "note": "Latest release (2022) of the associated JASPAR database.", "metadata": { "title": "JASPAR 2022: The 9th release of the open-access database of transcription factor binding profiles", "abstract": "JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.", "date": "2022-01-07T00:00:00Z", "citationCount": 356, "authors": [ { "name": "Castro-Mondragon J.A." }, { "name": "Riudavets-Puig R." }, { "name": "Rauluseviciute I." }, { "name": "Berhanu Lemma R." }, { "name": "Turchi L." }, { "name": "Blanc-Mathieu R." }, { "name": "Lucas J." }, { "name": "Boddie P." }, { "name": "Khan A." }, { "name": "Perez N.M." }, { "name": "Fornes O." }, { "name": "Leung T.Y." }, { "name": "Aguirre A." }, { "name": "Hammal F." }, { "name": "Schmelter D." }, { "name": "Baranasic D." }, { "name": "Ballester B." }, { "name": "Sandelin A." }, { "name": "Lenhard B." }, { "name": "Vandepoele K." }, { "name": "Wasserman W.W." }, { "name": "Parcy F." }, { "name": "Mathelier A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkx1188", "pmid": "29140473", "pmcid": "PMC5753243", "type": [ "Other" ], "version": "1", "note": "Release that introduced the JASPAR RESTful API.", "metadata": { "title": "Erratum: JASPAR 2018: Update of the open-access database of transcription factor binding profiles and its web framework (Nucleic Acids Research (2017) DOI: 10.1093/nar/gkx1126)", "abstract": "The above paper was corrected to add a reference to its companion paper: Chéneby, J., Gheorghe, M.,Artufel,M.,Mathelier, A., Ballester, B. (2017) ReMap 2018: An updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. 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"Installation instructions", "Release notes" ], "note": null } ], "publication": [ { "doi": "10.1038/s42256-021-00413-z", "pmid": "37396030", "pmcid": "PMC10312379", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires", "abstract": "Adaptive immune receptor repertoires (AIRR) are key targets for biomedical research as they record past and ongoing adaptive immune responses. The capacity of machine learning (ML) to identify complex discriminative sequence patterns renders it an ideal approach for AIRR-based diagnostic and therapeutic discovery. So far, widespread adoption of AIRR ML has been inhibited by a lack of reproducibility, transparency and interoperability. immuneML (immuneml.uio.no) addresses these concerns by implementing each step of the AIRR ML process in an extensible, open-source software ecosystem that is based on fully specified and shareable workflows. To facilitate widespread user adoption, immuneML is available as a command-line tool and through an intuitive Galaxy web interface, and extensive documentation of workflows is provided. We demonstrate the broad applicability of immuneML by (1) reproducing a large-scale study on immune state prediction, (2) developing, integrating and applying a novel deep learning method for antigen specificity prediction and (3) showcasing streamlined interpretability-focused benchmarking of AIRR ML.", "date": "2021-11-01T00:00:00Z", "citationCount": 17, "authors": [ { "name": "Pavlovic M." }, { "name": "Scheffer L." }, { "name": "Motwani K." }, { "name": "Kanduri C." }, { "name": "Kompova R." }, { "name": "Vazov N." }, { "name": "Waagan K." }, { "name": "Bernal F.L.M." }, { "name": "Costa A.A." }, { "name": "Corrie B." }, { "name": "Akbar R." }, { "name": "Al Hajj G.S." }, { "name": "Balaban G." }, { "name": "Brusko T.M." }, { "name": "Chernigovskaya M." }, { "name": "Christley S." }, { "name": "Cowell L.G." }, { "name": "Frank R." }, { "name": "Grytten I." }, { "name": "Gundersen S." }, { "name": "Haff I.H." }, { "name": "Hovig E." }, { "name": "Hsieh P.-H." }, { "name": "Klambauer G." }, { "name": "Kuijjer M.L." }, { "name": "Lund-Andersen C." }, { "name": "Martini A." }, { "name": "Minotto T." }, { "name": "Pensar J." }, { "name": "Rand K." }, { "name": "Riccardi E." }, { "name": "Robert P.A." }, { "name": "Rocha A." }, { "name": "Slabodkin A." }, { "name": "Snapkov I." }, { "name": "Sollid L.M." }, { "name": "Titov D." }, { "name": "Weber C.R." }, { "name": "Widrich M." }, { "name": "Yaari G." }, { "name": "Greiff V." }, { "name": "Sandve G.K." } ], "journal": "Nature Machine Intelligence" } } ], "credit": [ { "name": "Sandve Research Group for Biomedical Informatics", "email": "contact@immuneml.uio.no", "url": "https://sandvelab.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer", "Support" ], "note": null }, { "name": "Geir Kjetil Sandve", "email": "geirksa@ifi.uio.no", "url": "https://www.mn.uio.no/sbi/english/groups/sandve-group/", "orcidid": "https://orcid.org/0000-0002-4959-1409", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer", "Support" ], "note": null }, { "name": "Milena Pavlović", "email": "contact@immuneml.uio.no", "url": null, "orcidid": "https://orcid.org/0000-0002-2484-3868", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Documentor" ], "note": null }, { "name": "Lonneke Scheffer", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-8900-075X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Documentor" ], "note": null }, { "name": "Keshav Motwani", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-1457-2731", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "University of Oslo", "email": null, "url": null, "orcidid": null, "gridid": "grid.55325.34", "rorid": "00j9c2840", "fundrefid": "10.13039/501100005366", "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk", "email": "support@elixir.no", "url": "https://elixir.no/helpdesk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Support" ], "note": null }, { "name": "Victor Greiff", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-2622-5032", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Rahmad Akbar", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6692-0876", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Ghadi S. 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Weber", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-4802-8996", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Michael Widrich", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-5721-0135", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Erin Calhoun", "email": "erin.calhoun@uit.no", "url": null, "orcidid": "https://orcid.org/0009-0003-3752-7156", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": "Curation of bio.tools profile - please contact me with updates/corrections" } ], "community": null, "owner": "Kigaard", "additionDate": "2021-09-27T08:24:14.939476Z", "lastUpdate": "2023-08-04T08:01:14.040850Z", "editPermission": { "type": "group", "authors": [ "eca008" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "CHOPCHOP", "description": "CHOPCHOP is a versatile tool for selecting target sites for CRISPR (Cas9, Cas9 nickase, Cas13, Cpf1/CasX) or TALEN-directed mutagenesis. The latest release of CHOPCHOP (version 3) includes many new features and visualization options, supporting over 200 genomes with whole-gene targeting and versatile search modes. The tool now enables precise RNA targeting with Cas13, supporting alternative transcript isoforms and predicting RNA accessibility using ViennaRNA's RNAfold. The update also introduces new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. For larger queries or handling unsupported genomes, a command-line version is available with additional functionalities. 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The technology was initially developed to induce targeted mutations in DNA, but CRISPR-Cas has now been adapted to target nucleic acids for a range of purposes. CHOPCHOP is a web tool for identifying CRISPR-Cas single guide RNA (sgRNA) targets. In this major update of CHOPCHOP, we expand our toolbox beyond knockouts. We introduce functionality for targeting RNA with Cas13, which includes support for alternative transcript isoforms and RNA accessibility predictions. We incorporate new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. Finally, we expand our results page visualization to reveal alternative isoforms and downstream ATG sites, which will aid users in avoiding the expression of truncated proteins. The CHOPCHOP web tool now supports over 200 genomes and we have released a command-line script for running larger jobs and handling unsupported genomes. CHOPCHOP v3 can be found at https://chopchop.cbu.uib.no", "date": "2019-07-01T00:00:00Z", "citationCount": 600, "authors": [ { "name": "Labun K." }, { "name": "Montague T.G." }, { "name": "Krause M." }, { "name": "Torres Cleuren Y.N." }, { "name": "Tjeldnes H." }, { "name": "Valen E." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1002/cpz1.46", "pmid": "33905612", "pmcid": null, "type": [ "Usage" ], "version": "3", "note": null, "metadata": { "title": "CRISPR Genome Editing Made Easy Through the CHOPCHOP Website", "abstract": "The design of optimal guide RNA (gRNA) sequences for CRISPR systems is challenged by the need to achieve highly efficient editing at the desired location (on-target editing) with minimal editing at unintended locations (off-target editing). Although laboratory validation should ideally be used to detect off-target activity, computational predictions are almost always preferred in practice due to their speed and low cost. Several studies have therefore explored gRNA-DNA interactions in order to understand how CRISPR complexes select their genomic targets. CHOPCHOP (https://chopchop.cbu.uib.no/) leverages these developments to build a user-friendly web interface that helps users design optimal gRNAs. CHOPCHOP supports a wide range of CRISPR applications, including gene knock-out, sequence knock-in, and RNA knock-down. Furthermore, CHOPCHOP offers visualization that enables an informed choice of gRNAs and supports experimental validation. In these protocols, we describe the best practices for gRNA design using CHOPCHOP. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Design of gRNAs for gene knock-out. Alternate Protocol 1: Design of gRNAs for dCas9 fusion/effector targeting. Support Protocol: Design of gRNAs for targeting transgenic or plasmid sequences. Basic Protocol 2: Design of gRNAs for RNA targeting. Basic Protocol 3: Design of gRNAs for sequence knock-in. Alternate Protocol 2: Design of gRNAs for knock-in using non-homologous end joining. Basic Protocol 4: Design of gRNAs for knock-in using Cas9 nickases.", "date": "2021-04-01T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Labun K." }, { "name": "Krause M." }, { "name": "Torres Cleuren Y." }, { "name": "Valen E." } ], "journal": "Current Protocols" } }, { "doi": "10.1093/nar/gkw398", "pmid": "27185894", "pmcid": "PMC4987937", "type": [ "Primary" ], "version": "2", "note": null, "metadata": { "title": "CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering", "abstract": "In just 3 years CRISPR genome editing has transformed biology, and its popularity and potency continue to grow. New CRISPR effectors and rules for locating optimum targets continue to be reported, highlighting the need for computational CRISPR targeting tools to compile these rules and facilitate target selection and design. CHOPCHOP is one of the most widely used web tools for CRISPR- and TALEN-based genome editing. Its overarching principle is to provide an intuitive and powerful tool that can serve both novice and experienced users. In this major update we introduce tools for the next generation of CRISPR advances, including Cpf1 and Cas9 nickases. We support a number of new features that improve the targeting power, usability and efficiency of CHOPCHOP. To increase targeting range and specificity we provide support for custom length sgRNAs, and we evaluate the sequence composition of the whole sgRNA and its surrounding region using models compiled from multiple large-scale studies. These and other new features, coupled with an updated interface for increased usability and support for a continually growing list of organisms, maintain CHOPCHOP as one of the leading tools for CRISPR genome editing. CHOPCHOP v2 can be found at http://chopchop.cbu.uib.no.", "date": "2016-07-08T00:00:00Z", "citationCount": 552, "authors": [ { "name": "Labun K." }, { "name": "Montague T.G." }, { "name": "Gagnon J.A." }, { "name": "Thyme S.B." }, { "name": "Valen E." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gku410", "pmid": "24861617", "pmcid": "PMC4086086", "type": [ "Primary" ], "version": "1", "note": null, "metadata": { "title": "CHOPCHOP: A CRISPR/Cas9 and TALEN web tool for genome editing", "abstract": "Major advances in genome editing have recently been made possible with the development of the TALEN and CRISPR/Cas9 methods. The speed and ease of implementing these technologies has led to an explosion of mutant and transgenic organisms. A rate-limiting step in efficiently applying TALEN and CRISPR/Cas9 methods is the selection and design of targeting constructs. We have developed an online tool, CHOPCHOP (https://chopchop.rc.fas.harvard.edu), to expedite the design process. CHOPCHOP accepts a wide range of inputs (gene identifiers, genomic regions or pasted sequences) and provides an array of advanced options for target selection. It uses efficient sequence alignment algorithms to minimize search times, and rigorously predicts off-target binding of single-guide RNAs (sgRNAs) and TALENs. Each query produces an interactive visualization of the gene with candidate target sites displayed at their genomic positions and color-coded according to quality scores. In addition, for each possible target site, restriction sites and primer candidates are visualized, facilitating a streamlined pipeline of mutant generation and validation. The ease-of-use and speed of CHOPCHOP make it a valuable tool for genome engineering. © 2014 The Author(s).", "date": "2014-07-01T00:00:00Z", "citationCount": 736, "authors": [ { "name": "Montague T.G." }, { "name": "Cruz J.M." }, { "name": "Gagnon J.A." }, { "name": "Church G.M." }, { "name": "Valen E." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Kornel Labun", "email": "kornel.labun@uib.no", "url": null, "orcidid": "https://orcid.org/0000-0002-1262-2611", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer", "Support" ], "note": null }, { "name": "Tessa Montague", "email": "tessa.chopchop@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0002-5918-6327", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Contributor", "Support" ], "note": null }, { "name": "Valen Group (Computational Biology Unit)", "email": null, "url": "https://www.cbu.uib.no/valen/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Developer", "Maintainer", "Support" ], "note": null }, { "name": "The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk", "email": "support@elixir.no", "url": "https://elixir.no/helpdesk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Support" ], "note": "Helpdesk and support for ELIXIR Norway services" }, { "name": "University of Bergen", "email": null, "url": "https://www.uib.no/en", "orcidid": null, "gridid": "grid.7914.b", "rorid": "03zga2b32", "fundrefid": "10.13039/501100005036", "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "James Graham", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-8639-7592", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Recommendations on the long-read enrichment mode" }, { "name": "Bergen Research Foundation", "email": null, "url": "https://mohnfoundation.no/en/about/", "orcidid": null, "gridid": "grid.478482.5", "rorid": "04efaep75", "fundrefid": "10.13039/501100006475", "typeEntity": "Funding agency", "typeRole": [], "note": "Now part of the Trond Mohn Foundation" }, { "name": "University of Bergen", "email": null, "url": "https://www.uib.no/en", "orcidid": null, "gridid": "grid.7914.b", "rorid": "03zga2b32", "fundrefid": "10.13039/501100005036", "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "The Research Council of Norway", "email": null, "url": "http://www.forskningsradet.no/en/Home_page/1177315753906", "orcidid": null, "gridid": "grid.13985.36", "rorid": "00epmv149", "fundrefid": "10.13039/501100005416", "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "Erin Calhoun", "email": "erin.calhoun@uit.no", "url": null, "orcidid": "https://orcid.org/0009-0003-3752-7156", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": "Curation of bio.tools profile - contact me with updates/corrections." } ], "community": null, "owner": "edv", "additionDate": "2016-03-11T10:35:00Z", "lastUpdate": "2023-08-03T13:19:40.201053Z", "editPermission": { "type": "group", "authors": [ "eca008" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WEBnma", "description": "WEBnm@ provides quick, automated computation and analysis of low-frequency normal modes for protein structures.", "homepage": "http://apps.cbu.uib.no/webnma", "biotoolsID": "webnma", "biotoolsCURIE": "biotools:webnma", "version": [ "3.5" ], "otherID": [], "relation": [ { "biotoolsID": "numpy", "type": "uses" }, { "biotoolsID": "biopython", "type": "uses" }, { "biotoolsID": "matplotlib", "type": "uses" }, { "biotoolsID": "mustang", "type": "uses" }, { "biotoolsID": "dssp", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_0244", "term": "Protein flexibility and motion analysis" } ], "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_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_1354", "term": "Sequence profile" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Constructs elastic network model from alpha carbon coordinates of the protein, and computes properties to describe large scale conformations. Computes normal modes, fluctuation profiles, inter-residue correlations, conformational overlap analysis and vector field representations. Structural amino acid profiles, and normal mode characteristics describing protein motion, visualized in plots and decorated structure visualizations. White space delimited tabular data for normal modes and the provided plots", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2487", "term": "Protein structure comparison" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0886", "term": "Structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" } ] }, { "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_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_0889", "term": "Structural profile" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Performs comparative analysis of the normal modes of protein structures. Computes the Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner Product (RMSIP) of aligned parts of the proteins. Alignment of sets of proteins to be compared. Multiple protein structures Heatmaps, dendrograms and structural amino acid profiles for visual comparison of structural similarity. White space delimited tabular data for the provided plots", "cmd": null } ], "toolType": [ "Web API", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "BiB tools", "CBU tools", "UiB tools", "ELIXIR-NO", "ELIXIR-Norway" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Norway" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "https://github.com/reuter-group/webnma3", "type": [ "Repository", "Issue tracker" ], "note": null }, { "url": "https://elixir.no/helpdesk", "type": [ "Helpdesk" ], "note": "Helpdesk and support for ELIXIR Norway services." } ], "download": [], "documentation": [ { "url": "http://apps.cbu.uib.no/webnma3/howto/single", "type": [ "Quick start guide" ], "note": null }, { "url": "http://apps.cbu.uib.no/webnma3/qanda", "type": [ "FAQ" ], "note": null }, { "url": "http://apps.cbu.uib.no/webnma3/about", "type": [ "General", "Citation instructions" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-014-0427-6", "pmid": "25547242", "pmcid": "PMC4339738", "type": [ "Primary" ], "version": "2.0", "note": null, "metadata": { "title": "WEBnmat v2.0: Web server and services for comparing protein flexibility", "abstract": "Background: Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. Results: We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnmat, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the. In addition, programmatic access to WEBnmat is now available through a SOAP-based web service. WEBnmat is available at. Conclusion: WEBnmat v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnmat facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.", "date": "2014-12-30T00:00:00Z", "citationCount": 70, "authors": [ { "name": "Tiwari S.P." }, { "name": "Fuglebakk E." }, { "name": "Hollup S.M." }, { "name": "Skjaerven L." }, { "name": "Cragnolini T." }, { "name": "Grindhaug S.H." }, { "name": "Tekle K.M." }, { "name": "Reuter N." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1186/1471-2105-6-52", "pmid": "15762993", "pmcid": "PMC1274249", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "WEBnm@: A web application for normal mode analyses of proteins", "abstract": "Background: Normal mode analysis (NMA) has become the method of choice to investigate the slowest motions in macromolecular systems. NMA is especially useful for large biomolecular assemblies, such as transmembrane channels or virus capsids. NMA relies on the hypothesis that the vibrational normal modes having the lowest frequencies (also named soft modes) describe the largest movements in a protein and are the ones that are functionally relevant. Results: We developed a web-based server to perform normal modes calculations and different types of analyses. Starting from a structure file provided by the user in the PDB format, the server calculates the normal modes and subsequently offers the user a series of automated calculations; normalized squared atomic displacements, vector field representation and animation of the first six vibrational modes. Each analysis is performed independently from the others and results can be visualized using only a web browser. No additional plug-in or software is required. For users who would like to analyze the results with their favorite software, raw results can also be downloaded. The application is available on http://www.bioinfo.no/tools/normalmodes. We present here the underlying theory, the application architecture and an illustration of its features using a large transmembrane protein as an example. Conclusion: We built an efficient and modular web application for normal mode analysis of proteins. Non specialists can easily and rapidly evaluate the degree of flexibility of multi-domain protein assemblies and characterize the large amplitude movements of their domains. © 2005 Hollup et al; licensee BioMed Central Ltd.", "date": "2005-03-11T00:00:00Z", "citationCount": 103, "authors": [ { "name": "Hollup S.M." }, { "name": "Salensminde G." }, { "name": "Reuter N." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Nathalie Reuter", "email": "Nathalie.Reuter@uib.no", "url": "http://www.cbu.uib.no/reuter/", "orcidid": "https://orcid.org/0000-0002-3649-7675", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Sandhya P Tiwari", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-0747-3826", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Kidane M Tekle", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Tristan Cragnolini", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Svenn H Grindhaug", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Lars Skjærven", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Gisle Salensminde", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Edvin Fuglebakk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Siv M Hollup", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Department of Molecular Biology, University of Bergen, Norway", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Computational Biology Unit, Department of Informatics, University of Bergen, Norway", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "UiB", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "community": null, "owner": "UiB", "additionDate": "2016-03-17T13:51:10Z", "lastUpdate": "2023-08-02T12:26:28.035500Z", "editPermission": { "type": "group", "authors": [ "eca008" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Salmobase", "description": "Salmobase provides a visual and analytic framework for molecular genomic resources dedicated to salmonid species, including Atlantic salmon and rainbow trout.", "homepage": "https://salmobase.org", "biotoolsID": "salmobase", "biotoolsCURIE": "biotools:salmobase", "version": [], "otherID": [], "relation": [ { "biotoolsID": "salmobase2", "type": "isNewVersionOf" }, { "biotoolsID": "jbrowse", "type": "includes" }, { "biotoolsID": "blast", "type": "includes" }, { "biotoolsID": "salmotifdb", "type": "includes" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3184", "term": "Sequence assembly visualisation" }, { "uri": "http://edamontology.org/operation_3208", "term": "Genome visualisation" }, { "uri": "http://edamontology.org/operation_0259", "term": "Sequence alignment comparison" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2093", "term": "Data reference" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1027", "term": "Gene ID (NCBI)" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1033", "term": "Ensembl gene ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1098", "term": "RefSeq accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2292", "term": "GenBank accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2154", "term": "Sequence name" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0919", "term": "Chromosome report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2787", "term": "NCBI genome accession" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_0925", "term": "Sequence assembly" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_3989", "term": "GZIP format" } ] }, { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [ { "uri": "http://edamontology.org/format_3989", "term": "GZIP format" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2909", "term": "Organism name" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_3266", "term": "Sequence assembly ID" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_1056", "term": "Database name" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1192", "term": "Tool name (BLAST)" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [ { "uri": "http://edamontology.org/format_1333", "term": "BLAST results" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3387", "term": "Marine biology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Norway" ], "elixirCommunity": [], "link": [ { "url": "https://gitlab.com/elixir-nmbu/salmobase", "type": [ "Repository", "Issue tracker" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s12864-017-3877-1", "pmid": "28651544", "pmcid": "PMC5485693", "type": [ "Primary" ], "version": "2017", "note": "Primary publication for an earlier version, then known as SalmoBase.", "metadata": { "title": "SalmoBase: An integrated molecular data resource for Salmonid species", "abstract": "Background: Salmonids are ray-finned fishes which constitute 11 genera and at least 70 species including Atlantic salmon, whitefishes, graylings, rainbow trout, and char. The common ancestor of all Salmonidae experienced a whole genome duplication (WGD) ~80 million years ago, resulting in an autotetraploid genome. Genomic rediplodization is still going on in salmonid species, providing an unique system for studying evolutionary consequences of whole genome duplication. In recent years, high quality genome sequences of Atlantic salmon and Rainbow trout has been established, due to their scientific and commercial values. In this paper we introduce SalmoBase ( http://www.salmobase.org/ ), a tool for making molecular resources for salmonids public available in a framework of visualizations and analytic tools. Results: SalmoBase has been developed as a part of the ELIXIR.NO project. Currently, SalmoBase contains molecular resources for Atlantic salmon and Rainbow trout. Data can be accessed through BLAST, Genome Browser (GBrowse), Genetic Variation Browser (GVBrowse) and Gene Expression Browser (GEBrowse). Conclusions: To the best of our knowledge, SalmoBase is the first database which integrates salmonids data and allow users to study salmonids in an integrated framework. The database and its tools (e.g., comparative genomics tools, synteny browsers) will be expanded as additional public resources describing other Salmonidae genomes become available.", "date": "2017-06-26T00:00:00Z", "citationCount": 40, "authors": [ { "name": "Samy J.K.A." }, { "name": "Mulugeta T.D." }, { "name": "Nome T." }, { "name": "Sandve S.R." }, { "name": "Grammes F." }, { "name": "Kent M.P." }, { "name": "Lien S." }, { "name": "Vage D.I." } ], "journal": "BMC Genomics" } }, { "doi": "10.1038/nature17164", "pmid": "27088604", "pmcid": "PMC8127823", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The Atlantic salmon genome provides insights into rediploidization", "abstract": "The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.", "date": "2016-04-18T00:00:00Z", "citationCount": 664, "authors": [ { "name": "Lien S." }, { "name": "Koop B.F." }, { "name": "Sandve S.R." }, { "name": "Miller J.R." }, { "name": "Kent M.P." }, { "name": "Nome T." }, { "name": "Hvidsten T.R." }, { "name": "Leong J.S." }, { "name": "Minkley D.R." }, { "name": "Zimin A." }, { "name": "Grammes F." }, { "name": "Grove H." }, { "name": "Gjuvsland A." }, { "name": "Walenz B." }, { "name": "Hermansen R.A." }, { "name": "Von Schalburg K." }, { "name": "Rondeau E.B." }, { "name": "Di Genova A." }, { "name": "Samy J.K.A." }, { "name": "Olav Vik J." }, { "name": "Vigeland M.D." }, { "name": "Caler L." }, { "name": "Grimholt U." }, { "name": "Jentoft S." }, { "name": "Inge Vage D." }, { "name": "De Jong P." }, { "name": "Moen T." }, { "name": "Baranski M." }, { "name": "Palti Y." }, { "name": "Smith D.R." }, { "name": "Yorke J.A." }, { "name": "Nederbragt A.J." }, { "name": "Tooming-Klunderud A." }, { "name": "Jakobsen K.S." }, { "name": "Jiang X." }, { "name": "Fan D." }, { "name": "Hu Y." }, { "name": "Liberles D.A." }, { "name": "Vidal R." }, { "name": "Iturra P." }, { "name": "Jones S.J.M." }, { "name": "Jonassen I." }, { "name": "Maass A." }, { "name": "Omholt S.W." }, { "name": "Davidson W.S." } ], "journal": "Nature" } } ], "credit": [ { "name": "Lars Grønvold", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-5404-4285", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk", "email": "support@elixir.no", "url": "https://elixir.no/helpdesk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Support" ], "note": null }, { "name": "Jeevan Karloss Antony Samy", "email": "jeevan.karloss@nmbu.no", "url": null, "orcidid": "https://orcid.org/0000-0002-8428-1481", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Amine Namouchi", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "community": null, "owner": "LarsGr", "additionDate": "2017-03-23T09:35:24Z", "lastUpdate": "2023-08-01T12:32:53.528664Z", "editPermission": { "type": "group", "authors": [ "eca008" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }