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"uri": "http://edamontology.org/operation_0239", "term": "Sequence motif recognition" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3497", "term": "DNA sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0849", "term": "Sequence record" }, "format": [ { "uri": "http://edamontology.org/format_1936", "term": "GenBank format" } ] }, { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "Single fasta file", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" }, { "uri": "http://edamontology.org/topic_0798", "term": "Mobile genetic elements" }, { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "GEM Pasteur" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/gem-pasteur/Integron_Finder/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "http://integronfinder.readthedocs.org/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkw319", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "1.5.1", "note": null, "metadata": { "title": "Identification and analysis of integrons and cassette arrays in bacterial genomes", "abstract": "Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program-IntegronFinder-to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as α-Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome.", "date": "2016-06-02T00:00:00Z", "citationCount": 193, "authors": [ { "name": "Cury J." }, { "name": "Jove T." }, { "name": "Touchon M." }, { "name": "Neron B." }, { "name": "Rocha E.P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.3390/microorganisms10020224", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "2.0.1", "note": null, "metadata": { "title": "Integron Functionality and Genome Innovation: An Update on the Subtle and Smart Strategy of Integrase and Gene Cassette Expression Regulation", "abstract": "Integrons are considered hot spots for bacterial evolution, since these platforms allow one-step genomic innovation by capturing and expressing genes that provide advantageous novelties, such as antibiotic resistance. The acquisition and shuffling of gene cassettes featured by integrons enable the population to rapidly respond to changing selective pressures. However, in order to avoid deleterious effects and fitness burden, the integron activity must be tightly controlled, which happens in an elegant and elaborate fashion, as discussed in detail in the present review. Here, we aimed to provide an up‐to‐date overview of the complex regulatory networks that permeate the expression and functionality of integrons at both transcriptional and translational levels. It was possible to compile strong shreds of evidence clearly proving that these versatile platforms include functions other than acquiring and expressing gene cassettes. The well‐balanced mechanism of integron expression is intricately related with environmental signals, host cell physiology, fitness, and survival, ultimately leading to adaptation on the demand.", "date": "2022-02-01T00:00:00Z", "citationCount": 9, "authors": [ { "name": "Fonseca E.L." }, { "name": "Vicente A.C." } ], "journal": "Microorganisms" } } ], "credit": [ { "name": "Institut Pasteur", "email": null, "url": "http://www.pasteur.fr/en", "orcidid": null, "gridid": "grid.428999.7", "rorid": "0495fxg12", "fundrefid": "10.13039/501100003762", "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "C3BI", "email": null, "url": "https://research.pasteur.fr/en/center/c3bi/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "ERC EVOMOBILOME", "email": null, "url": "https://erc.europa.eu/projects-and-results/erc-funded-projects/evomobilome", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jean Cury", "email": "jean.cury@normalesup.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Bertrand Neron", "email": "bneron@pasteur.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-0220-0482", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Eduardo Rocha", "email": "eduardo.rocha@pasteur.fr", "url": "https://research.pasteur.fr/fr/member/eduardo-rocha/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null }, { "name": "Microbial Evolutionary Genomics", "email": null, "url": "https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": "CNRS - UMR 352" }, { "name": "Jean Cury", "email": "jean.cury@normalesup.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Bertrand Neron", "email": "bneron@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Eduardo Rocha", "email": "eduardo.rocha@pasteur.fr", "url": "https://research.pasteur.fr/fr/member/eduardo-rocha/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Eloi Littner", "email": "eloi.littner@pasteur.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-8793-9584", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Matthieu Haudiquet", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-0878-2209", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Amandine PERRIN", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-4797-6185", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "INCEPTION", "email": null, "url": "https://anr.fr/ProjetIA-16-CONV-0005", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Laboratoire d’Excellence IBEID Integrative Biology of Emerging Infectious Diseases", "email": null, "url": "https://anr.fr/ProjetIA-10-LABX-0062", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null } ], "community": null, "owner": "jeanrjc", "additionDate": "2016-11-28T10:07:17Z", "lastUpdate": "2024-06-06T08:09:34.015441Z", "editPermission": { "type": "group", "authors": [ "hmenager", "khillion", "bneron" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DiversityNaviKey", "description": "The progressive web application DiversityNaviKey (DNK) is a generic tool primarily designed for any kind of diagnosis and interactive identification of organisms or other items as well as item groups which are part of or related to biodiversity, geodiversity or environmental research, by means of a set of pre-defined characteristics. It allows for sophisticated selection based on highly structured data sources (datasets) with descriptive data (trait data with descriptors, descriptor categorical states, descriptor values). The browser-based tool is optimized to build and run determination keys based on the consecutive selection of descriptors, descriptor states and values during the identification process. 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It approaches the problem by associating biochemical and electrophysiological data describing individual reactions with experimental microscopic image data describing their subcellular localizations. Individual processes are collected within a physical end computational infrastructure that accommodates any molecular mechanism expressible as rate equations or membrane fluxes. An illustration of the method is provided by a dynamic simulation of IP3-mediated Ca2+ release from endoplasmic reticulum in a neuronal cell. The results can be directly compared to experimental observations and provide insight into the role of experimentally inaccessible components of the overall mechanism.", "date": "1997-01-01T00:00:00Z", "citationCount": 207, "authors": [ { "name": "Schaff J." }, { "name": "Fink C.C." }, { "name": "Slepchenko B." }, { "name": "Carson J.H." }, { "name": "Loew L.M." } ], "journal": "Biophysical Journal" } }, { "doi": "10.1016/B978-0-12-388403-9.00008-4", "pmid": "22482950", "pmcid": "PMC3519356", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Spatial Modeling of Cell Signaling Networks", "abstract": "The shape of a cell, the sizes of subcellular compartments, and the spatial distribution of molecules within the cytoplasm can all control how molecules interact to produce a cellular behavior. This chapter describes how these spatial features can be included in mechanistic mathematical models of cell signaling. The Virtual Cell computational modeling and simulation software is used to illustrate the considerations required to build a spatial model. An explanation of how to appropriately choose between physical formulations that implicitly or explicitly account for cell geometry and between deterministic versus stochastic formulations for molecular dynamics is provided, along with a discussion of their respective strengths and weaknesses. As a first step toward constructing a spatial model, the geometry needs to be specified and associated with the molecules, reactions, and membrane flux processes of the network. Initial conditions, diffusion coefficients, velocities, and boundary conditions complete the specifications required to define the mathematics of the model. The numerical methods used to solve reaction-diffusion problems both deterministically and stochastically are then described and some guidance is provided in how to set up and run simulations. A study of cAMP signaling in neurons ends the chapter, providing an example of the insights that can be gained in interpreting experimental results through the application of spatial modeling. © 2012 Elsevier Inc.", "date": "2012-01-01T00:00:00Z", "citationCount": 94, "authors": [ { "name": "Cowan A.E." }, { "name": "Moraru I.I." }, { "name": "Schaff J.C." }, { "name": "Slepchenko B.M." }, { "name": "Loew L.M." } ], "journal": "Methods in Cell Biology" } }, { "doi": "10.1016/j.bpj.2017.08.022", "pmid": "28978431", "pmcid": "PMC5627391", "type": [ "Method" ], "version": null, "note": "Rule-based Models", "metadata": { "title": "Compartmental and Spatial Rule-Based Modeling with Virtual Cell", "abstract": "In rule-based modeling, molecular interactions are systematically specified in the form of reaction rules that serve as generators of reactions. This provides a way to account for all the potential molecular complexes and interactions among multivalent or multistate molecules. Recently, we introduced rule-based modeling into the Virtual Cell (VCell) modeling framework, permitting graphical specification of rules and merger of networks generated automatically (using the BioNetGen modeling engine) with hand-specified reaction networks. VCell provides a number of ordinary differential equation and stochastic numerical solvers for single-compartment simulations of the kinetic systems derived from these networks, and agent-based network-free simulation of the rules. In this work, compartmental and spatial modeling of rule-based models has been implemented within VCell. To enable rule-based deterministic and stochastic spatial simulations and network-free agent-based compartmental simulations, the BioNetGen and NFSim engines were each modified to support compartments. In the new rule-based formalism, every reactant and product pattern and every reaction rule are assigned locations. We also introduce the rule-based concept of molecular anchors. This assures that any species that has a molecule anchored to a predefined compartment will remain in this compartment. Importantly, in addition to formulation of compartmental models, this now permits VCell users to seamlessly connect reaction networks derived from rules to explicit geometries to automatically generate a system of reaction-diffusion equations. These may then be simulated using either the VCell partial differential equations deterministic solvers or the Smoldyn stochastic simulator.", "date": "2017-10-03T00:00:00Z", "citationCount": 28, "authors": [ { "name": "Blinov M.L." }, { "name": "Schaff J.C." }, { "name": "Vasilescu D." }, { "name": "Moraru I.I." }, { "name": "Bloom J.E." }, { "name": "Loew L.M." } ], "journal": "Biophysical Journal" } }, { "doi": "10.1371/journal.pcbi.1005236", "pmid": "27959915", "pmcid": null, "type": [ "Method" ], "version": null, "note": "Spatial Hybrid Deterministic-Stochastic Models", "metadata": { "title": "Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology", "abstract": "Hybrid deterministic-stochastic methods provide an efficient alternative to a fully stochastic treatment of models which include components with disparate levels of stochasticity. However, general-purpose hybrid solvers for spatially resolved simulations of reaction-diffusion systems are not widely available. Here we describe fundamentals of a general-purpose spatial hybrid method. The method generates realizations of a spatially inhomogeneous hybrid system by appropriately integrating capabilities of a deterministic partial differential equation solver with a popular particle-based stochastic simulator, Smoldyn. Rigorous validation of the algorithm is detailed, using a simple model of calcium ‘sparks’ as a testbed. The solver is then applied to a deterministic-stochastic model of spontaneous emergence of cell polarity. The approach is general enough to be implemented within biologist-friendly software frameworks such as Virtual Cell.", "date": "2016-12-01T00:00:00Z", "citationCount": 19, "authors": [ { "name": "Schaff J.C." }, { "name": "Gao F." }, { "name": "Li Y." }, { "name": "Novak I.L." }, { "name": "Slepchenko B.M." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Virtual Cell team", "email": "vcell_support@uchc.edu", "url": "https://vcell.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null }, { "name": "R24 GM137787 NIH/NIGMS", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null } ], "community": null, "owner": "mblinov", "additionDate": "2024-04-11T11:02:57.280432Z", "lastUpdate": "2024-04-15T16:38:22.115364Z", "editPermission": { "type": "private", "authors": [] 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"Primary" ], "version": "3.0", "note": null, "metadata": { "title": "HotSpot Wizard 3.0: Web server for automated design of mutations and smart libraries based on sequence input information", "abstract": "© The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.HotSpot Wizard is a web server used for the automated identification of hotspots in semi-rational protein design to give improved protein stability, catalytic activity, substrate specificity and enantioselectivity. Since there are three orders of magnitude fewer protein structures than sequences in bioinformatic databases, the major limitation to the usability of previous versions was the requirement for the protein structure to be a compulsory input for the calculation. HotSpot Wizard 3.0 now accepts the protein sequence as input data. The protein structure for the query sequence is obtained either from eight repositories of homology models or is modeled using Modeller and I-Tasser. The quality of the models is then evaluated using three quality assessment tools - WHAT-CHECK, PROCHECK and MolProbity. During follow-up analyses, the system automatically warns the users whenever they attempt to redesign poorly predicted parts of their homology models. The second main limitation of HotSpot Wizard's predictions is that it identifies suitable positions for mutagenesis, but does not provide any reliable advice on particular substitutions. A new module for the estimation of thermodynamic stabilities using the Rosetta and FoldX suites has been introduced which prevents destabilizing mutations among pre-selected variants entering experimental testing. HotSpot Wizard is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard.", "date": "2018-07-02T00:00:00Z", "citationCount": 43, "authors": [ { "name": "Sumbalova L." }, { "name": "Stourac J." }, { "name": "Martinek T." }, { "name": "Bednar D." }, { "name": "Damborsky J." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Jan Stourac", "email": "stourac.jan@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-3139-3700", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Support" ], "note": null }, { "name": "Jaroslav Bendl", "email": "jaroslav.bendl@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0001-9989-2720", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Lenka Sumbalova", "email": "lenka.sumbalova@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jan Brezovsky", "email": "brezovsky@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-9677-5078", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jiri Damborsky", "email": "1441@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-7848-8216", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Ondrej Vavra", "email": "o.vavra@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Eva Sebestova", "email": "40707@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Antonin Pavelka", "email": "99207@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Marie Jankujova", "email": "423826@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0003-3219-8149", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Loschmidt Laboratories", "email": null, "url": "https://loschmidt.chemi.muni.cz/peg/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Masaryk University, Brno, Czech Republic", "email": null, "url": "https://www.muni.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "International Centre for Clinical Research, Brno, Czech Republic", "email": null, "url": "https://www.fnusa-icrc.org/en/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Brno University of Technology, Brno, Czech Republic", "email": null, "url": "https://www.vutbr.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": "https://www.elixir-czech.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Provider" ], "note": null }, { "name": "HotSpot Wizard team", "email": "hsw@sci.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "European Commission", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Grant Agency of the Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Ministry of Education of the Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null } ], "community": null, "owner": "Loschmidt Laboratories", "additionDate": "2016-06-30T11:08:38Z", "lastUpdate": "2024-03-27T07:30:26.337722Z", "editPermission": { "type": "group", "authors": [ "YuanYue" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RiboGalaxy", "description": "Galaxy-based web server where researchers can pre-process, align, analyze and visualize their own ribosome profiling (ribo-seq) data. GUI-based tools are provided to determine the strength of the triplet periodicity signal in ribo-seq data, generate metagene and ribosome profiles and carry out differential translation expression analysis using the riboSeqR suite. The RUST suite of tools can be used to quickly characterize ribosome profiling datasets to assess their quality and more.", "homepage": "http://ribogalaxy.ucc.ie", "biotoolsID": "ribogalaxy", "biotoolsCURIE": "biotools:ribogalaxy", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2928", "term": "Alignment" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" }, { "uri": "http://edamontology.org/operation_2495", "term": "Gene expression analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0848", "term": "Raw sequence" }, "format": [ { "uri": "http://edamontology.org/format_1932", "term": "FASTQ-sanger" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_3006", "term": "bigWig" } ] }, { "data": { "uri": "http://edamontology.org/data_2969", "term": "Sequence image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] } ], "note": "Raw ribo-seq and mRNA-seq FASTQ files There are multiple outputs depending on the tool/jobs that are run. Most of the ribo-seq analysis tools provide the output in both spreadsheet and/or visual format.", "cmd": null } ], "toolType": [ "Workbench" ], "topic": [ { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" } ], "operatingSystem": [ "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [ "Galaxy" ], "link": [ { "url": "https://github.com/riboseqorg/RiboGalaxy", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "http://ribogalaxy.ucc.ie/static/conditions_of_use.html", "type": [ "Terms of use" ], "note": null }, { "url": "http://ribogalaxy.ucc.ie/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1080/15476286.2016.1141862", "pmid": "26821742", "pmcid": "PMC4829337", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "RiboGalaxy: A browser based platform for the alignment, analysis and visualization of ribosome profiling data", "abstract": "Ribosome profiling (ribo-seq) is a technique that uses high-throughput sequencing to reveal the exact locations and densities of translating ribosomes at the entire transcriptome level. The technique has become very popular since its inception in 2009. Yet experimentalists who generate ribo-seq data often have to rely on bioinformaticians to process and analyze their data. We present RiboGalaxy (http://ribogalaxy.ucc.ie), a freely available Galaxy-based web server for processing and analyzing ribosome profiling data with the visualization functionality provided by GWIPS-viz (http://gwips.ucc.ie). RiboGalaxy offers researchers a suite of tools specifically tailored for processing ribo-seq and corresponding mRNA-seq data. Researchers can take advantage of the published workflows which reduce the multi-step alignment process to a minimum of inputs from the user. Users can then explore their own aligned data as custom tracks in GWIPS-viz and compare their ribosome profiles to existing ribo-seq tracks from published studies. In addition, users can assess the quality of their ribo-seq data, determine the strength of the triplet periodicity signal, generate meta-gene ribosome profiles as well as analyze the relative impact of mRNA sequence features on local read density. RiboGalaxy is accompanied by extensive documentation and tips for helping users. In addition we provide a forum (http://gwips.ucc.ie/Forum) where we encourage users to post their questions and feedback to improve the overall RiboGalaxy service.", "date": "2016-03-03T00:00:00Z", "citationCount": 67, "authors": [ { "name": "Michel A.M." }, { "name": "Mullan J.P.A." }, { "name": "Velayudhan V." }, { "name": "O'Connor P.B.F." }, { "name": "Donohue C.A." }, { "name": "Baranov P.V." } ], "journal": "RNA Biology" } }, { "doi": "10.1016/J.JMB.2023.168043", "pmid": "37356899", "pmcid": null, "type": [ "Review" ], "version": null, "note": null, "metadata": { "title": "RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing – 2023 Update", "abstract": "Ribosome profiling (Ribo-Seq) captures a “snapshot” of ribosomes’ locations at the entire transcriptome of a cell at sub-codon resolution providing insights into gene expression and enabling the discovery of novel translated regions. RiboGalaxy (https://ribogalaxy.genomicsdatascience.ie/), a Galaxy-based platform for processing Ribo-Seq data is a RiboSeq.Org (https://riboseq.org/) resource. RiboSeq.Org is an online gateway to a set of integrated tools for the processing and analysis of Ribo-Seq data. In this RiboGalaxy update we introduce changes to both the tools available on RiboGalaxy and to how the resource is managed on the backend. For example, in order to improve interoperability between Riboseq.Org resources, we added tools that link RiboGalaxy outputs with Trips-Viz and GWIPS-viz browsers for downstream analysis and visualisation. RiboGalaxy's backend now utilises Ansible configuration management which enhances its stability and jobs are executed within Singularity containers and are managed by Slurm, strengthening reproducibility and performance respectively.", "date": "2023-07-15T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Fedorova A.D." }, { "name": "Tierney J.A.S." }, { "name": "Michel A.M." }, { "name": "Baranov P.V." } ], "journal": "Journal of Molecular Biology" } } ], "credit": [ { "name": "Science Foundation Ireland", "email": "info@sfi.ie", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "ucc.ie", "email": null, "url": "http://www.ucc.ie", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "ribogalaxy@gmail.com", "url": "http://ribogalaxy.ucc.ie/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Pavel V. Baranov", "email": "p.baranov@ucc.ie", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "A.Michel@ucc.ie", "additionDate": "2016-05-24T10:51:12Z", "lastUpdate": "2024-02-23T09:02:01.891026Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AltaiR", "description": "AltaiR is a C toolkit for alignment-free and spatial-temporal analysis of multi-FASTA data.\n\nThis method provides alignment-free and spatial-temporal analysis of multi-FASTA data through the implementation of a C toolkit that is highly flexible and with characteristics covering large-scale data, namely extensive collections of genomes/proteomes. This toolkit is ideal for scenarios entangling the presence of multiple sequences from epidemic and pandemic events. AlcoR is implemented in C language using multi-threading to increase the computational speed, is flexible for multiple applications, and does not contain external dependencies. The tool accepts any sequence(s) in (multi-) FASTA format.", "homepage": "https://github.com/cobilab/altair", "biotoolsID": "altair", "biotoolsCURIE": "biotools:altair", "version": [ "1.0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_3303", "term": "Medicine" } ], "operatingSystem": [ "Linux" ], "language": [ "C" ], "license": "GPL-3.0", "collectionID": [ "COVID-19", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Data" ], "elixirNode": [ "Portugal" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/cobilab/altair", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Jorge M. Silva", "email": "jorge.miguel.ferreira.silva@ua.pt", "url": null, "orcidid": "http://orcid.org/0000-0002-6331-6091", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Contributor" ], "note": "Researcher at IEETA. J.M.S. has received funding from the EC under grant agreement 101081813, Genomic Data Infrastructure." }, { "name": "Diogo Pratas", "email": "pratas@ua.pt", "url": null, "orcidid": "http://orcid.org/0000-0003-1176-552X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": "Researcher at IEETA. D.P. is funded by national funds through FCT – Fundação para a Ciência e a Tecnologia, I.P., under the Scientific Employment Stimulus - Institutional Call - reference CEECINST/00026/2018." } ], "community": null, "owner": "jorgeMFS", "additionDate": "2023-12-13T14:54:35.138186Z", "lastUpdate": "2023-12-13T14:54:35.146893Z", "editPermission": { "type": "group", "authors": [ "pratas" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MrBayes", "description": "Program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.", "homepage": "http://nbisweden.github.io/MrBayes/", "biotoolsID": "mrbayes", "biotoolsCURIE": "biotools:mrbayes", "version": [ "3.2.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0547", "term": "Phylogenetic tree generation (maximum likelihood and Bayesian methods)" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/NBISweden/MrBayes", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/NBISweden/MrBayes/releases/tag/v3.2.6", "type": "Source code", "note": null, "version": null }, { "url": "https://github.com/NBISweden/MrBayes/releases/tag/v3.2.6", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/NBISweden/MrBayes/blob/develop/COPYING", "type": [ "Terms of use" ], "note": null }, { "url": "http://nbisweden.github.io/MrBayes/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/17.8.754", "pmid": "11524383", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MRBAYES: Bayesian inference of phylogenetic trees", "abstract": "Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo.", "date": "2001-01-01T00:00:00Z", "citationCount": 18632, "authors": [ { "name": "Huelsenbeck J.P." }, { "name": "Ronquist F." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/bioinformatics/btg180", "pmid": "12912839", "pmcid": null, "type": [], "version": "3", "note": null, "metadata": { "title": "MrBayes 3: Bayesian phylogenetic inference under mixed models", "abstract": "Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types - e.g. morphological, nucleotide, and protein - and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.", "date": "2003-08-12T00:00:00Z", "citationCount": 24269, "authors": [ { "name": "Ronquist F." }, { "name": "Huelsenbeck J.P." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/sysbio/sys029", "pmid": "22357727", "pmcid": "PMC3329765", "type": [], "version": "3.2", "note": null, "metadata": { "title": "Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space", "abstract": "Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site dN/dS rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software. © 2012 The Author(s).", "date": "2012-05-01T00:00:00Z", "citationCount": 15381, "authors": [ { "name": "Ronquist F." }, { "name": "Teslenko M." }, { "name": "Van Der Mark P." }, { "name": "Ayres D.L." }, { "name": "Darling A." }, { "name": "Hohna S." }, { "name": "Larget B." }, { "name": "Liu L." }, { "name": "Suchard M.A." }, { "name": "Huelsenbeck J.P." } ], "journal": "Systematic Biology" } } ], "credit": [ { "name": "Fredrik Ronquist", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Paul van der Mark", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Maxim Teslenko", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Donald Simon", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "John Huelsenbeck", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Bret Larget", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Chi Zhang", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Dept. of Biodiversity Informatics at the Swedish Museum of Natural History", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Vetenskapsrådet", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "NSF", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "NIH", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "icm.uu.se", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "http://nbisweden.github.io/MrBayes/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "andreas.kahari@icm.uu.se", "additionDate": "2016-04-21T06:14:09Z", "lastUpdate": "2023-11-03T08:32:13.053903Z", "editPermission": { "type": "group", "authors": [ "sergitobara", "EngyNasr" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Clustal 2 (Clustal W, Clustal X)", "description": "Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). 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