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{ "count": 1114, "next": "?page=2", "previous": null, "list": [ { "name": "REPET", "description": "The REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyze transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii)\n TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.", "homepage": "https://urgi.versailles.inrae.fr/Tools/REPET", "biotoolsID": "repet", "biotoolsCURIE": "biotools:repet", "version": [ "v3.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0379", "term": "Repeat sequence detection" }, { "uri": "http://edamontology.org/operation_0237", "term": "Repeat sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "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_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" } ] }, { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_1939", "term": "GFF3-seq" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0157", "term": "Sequence composition, complexity and repeats" }, { "uri": "http://edamontology.org/topic_0654", "term": "DNA" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "C++", "Python" ], "license": "CECILL-2.0", "collectionID": [ "REPET", "elixir-fr-sdp-2019", "PlantBioinfoPF", "URGI" ], "maturity": "Legacy", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://urgi.versailles.inrae.fr/download/repet/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://urgi.versailles.inrae.fr/download/repet/REPET_linux-x64-3.0.tar.gz", "type": "Source code", "note": null, "version": "v3.0" } ], "documentation": [ { "url": "https://urgi.versailles.inrae.fr/Tools/REPET", "type": [ "General" ], "note": "see also https://urgi.versailles.inrae.fr/Tools/REPET/README" }, { "url": "https://urgi.versailles.inrae.fr/Tools/REPET/INSTALL", "type": [ "Installation instructions" ], "note": null }, { "url": "https://urgi.versailles.inrae.fr/Tools/REPET/TEdenovo-tuto", "type": [ "User manual" ], "note": "See also https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto" }, { "url": "https://forgemia.inra.fr/urgi-anagen/wiki-repet/-/wikis/REPET-V3.0-tutorial", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0091929", "pmid": "24786468", "pmcid": "PMC4008368", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PASTEC: An automatic transposable element classification tool", "abstract": "Summary: The classification of transposable elements (TEs) is key step towards deciphering their potential impact on the genome. However, this process is often based on manual sequence inspection by TE experts. With the wealth of genomic sequences now available, this task requires automation, making it accessible to most scientists. We propose a new tool, PASTEC, which classifies TEs by searching for structural features and similarities. This tool outperforms currently available software for TE classification. The main innovation of PASTEC is the search for HMM profiles, which is useful for inferring the classification of unknown TE on the basis of conserved functional domains of the proteins. In addition, PASTEC is the only tool providing an exhaustive spectrum of possible classifications to the order level of the Wicker hierarchical TE classification system. It can also automatically classify other repeated elements, such as SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. Finally, the output of this new tool is designed to facilitate manual curation by providing to biologists with all the evidence accumulated for each TE consensus. Availability: PASTEC is available as a REPET module or standalone software (http://urgi.versailles.inra.fr/download/repet/REPET-linux-x64-2.2.tar. gz). It requires a Unix-like system. There are two standalone versions: one of which is parallelized (requiring Sun grid Engine or Torque), and the other of which is not. © 2014 Hoede et al.", "date": "2014-05-02T00:00:00Z", "citationCount": 203, "authors": [ { "name": "Hoede C." }, { "name": "Arnoux S." }, { "name": "Moisset M." }, { "name": "Chaumier T." }, { "name": "Inizan O." }, { "name": "Jamilloux V." }, { "name": "Quesneville H." } ], "journal": "PLoS ONE" } }, { "doi": "10.1371/journal.pone.0016526", "pmid": "21304975", "pmcid": "PMC3031573", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Considering transposable element diversification in de novo annotation approaches", "abstract": "Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of highthroughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species. © 2011 Flutre et al.", "date": "2011-02-09T00:00:00Z", "citationCount": 330, "authors": [ { "name": "Flutre T." }, { "name": "Duprat E." }, { "name": "Feuillet C." }, { "name": "Quesneville H." } ], "journal": "PLoS ONE" } }, { "doi": "10.1371/journal.pcbi.0010022", "pmid": "16110336", "pmcid": "PMC1185648", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Combined evidence annotation of transposable elements in genome sequences", "abstract": "Transposable elements (TEs) are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated \"TE models\" in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1), and we found a substantially higher number of TEs (n = 6,013) than previously identified (n = 1,572). Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1). We also estimated that 518 TE copies (8.6%) are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other species in the genus Drosophila. © 2005 Quesneville et al.", "date": "2005-01-01T00:00:00Z", "citationCount": 262, "authors": [ { "name": "Quesneville H." }, { "name": "Bergman C.M." }, { "name": "Andrieu O." }, { "name": "Autard D." }, { "name": "Nouaud D." }, { "name": "Ashburner M." }, { "name": "Anxolabehere D." } ], "journal": "PLoS Computational Biology" } }, { "doi": "10.1007/s00239-003-0007-2", "pmid": "15008403", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes", "abstract": "The techniques that are usually used to detect transposable elements (TEs) in nucleic acid sequences rely on sequence similarity with previously characterized elements. However, these methods are likely to miss many elements in various organisms. We tested two strategies for the detection of unknown elements. The first, which we call \"TBLASTX strategy,\" searches for TE sequences by comparing the six-frame translations of the nucleic acid sequences of known TEs with the genomic sequence of interest. The second, \"repeat-based strategy,\" searches genomic sequences for long repeats and clusters them in groups of similar sequences. TE copies from a given family are expected to cluster together. We tested the Drosophila melanogaster genomic sequence and the recently sequenced Anopheles gambiae genome in which most TEs remain unknown. We showed that the \"TBLASTX strategy\" is very efficient as it detected at least 332 new TE families in D. melanogaster and 400 in A. gambiae. This was unexpected in Drosophila as TEs of this organism have been extensively studied. The \"repeat-based strategy\" appeared to be very inefficient because of two problems: (i) TE copies are heavily deleted and few copies share homologous regions, and (ii) segmental duplications are frequent and it is not easy to distinguish them from TE copies.", "date": "2003-12-29T00:00:00Z", "citationCount": 62, "authors": [ { "name": "Quesneville H." }, { "name": "Nouaud D." }, { "name": "Anxolabehere D." } ], "journal": "Journal of Molecular Evolution" } }, { "doi": "10.1109/JPROC.2016.2590833", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue", "abstract": "Transposable elements (TEs) constitute the most dynamic and the largest component of large plant genomes: for example, 80% to 90% of the maize genome and the wheat genome may be TEs. De novo TE annotation is therefore a computational challenge, and we investigated, using current tools in the REPET package, new strategies to overcome the difficulties. We tested our methodological developments on the sequence of the chromosome 3B of the hexaploid wheat; this chromosome is ~1 Gb, one of the 'fattest' genomes ever sequenced. We successfully established various strategies for annotating TEs in such a complex dataset. Our analyses show that all of our strategies can overcome the current limitations for de novo TE discovery in large plant genomes. Relative to annotation based on a library of known TEs, our de novo approaches improved genome coverage (from 84% to 90%), and the number of full length annotated copies from 14 830 to 15 905. We also developed two new metrics for qualifying TE annotation: NTE50 involves measuring the number, and LTE50 the smallest sizes of annotations that cover 50% of the genome. NTE50 decreased the number of annotations from 124 868 to 93 633 and LTE50 increased it from 1839 to 2659. This work shows how to obtain comprehensive and high-quality automatic TE annotation for a number of economically and agronomically important species.", "date": "2017-03-01T00:00:00Z", "citationCount": 15, "authors": [ { "name": "Jamilloux V." }, { "name": "Daron J." }, { "name": "Choulet F." }, { "name": "Quesneville H." } ], "journal": "Proceedings of the IEEE" } } ], "credit": [ { "name": "URGI", "email": "urgi-repet@versailles.inrae.fr", "url": "http://urgi.versailles.inrae.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Developer", "Contributor", "Maintainer", "Provider", "Support", "Documentor" ], "note": "This tool has a \"Numero de depot APP\": FR 001 480007 000 R P 2008 000 31 235" } ], "community": null, "owner": "Institut Francais de Bioinform", "additionDate": "2016-03-24T16:22:28Z", "lastUpdate": "2024-09-06T17:39:57.162017Z", "editPermission": { "type": "group", "authors": [ "vjamilloux", "johann_confais", "raphael.flores" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "TrieDedup", "description": "A fast trie-based deduplication algorithm to handle ambiguous bases in high-throughput sequencing.", "homepage": "https://github.com/lolrenceH/TrieDedup", "biotoolsID": "triededup", "biotoolsCURIE": "biotools:triededup", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" }, { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_3519", "term": "PCR experiment" } ], "operatingSystem": [], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s12859-024-05775-w", "pmid": "38637756", "pmcid": "PMC11025179", "type": [], "version": null, "note": null, "metadata": { "title": "TrieDedup: a fast trie-based deduplication algorithm to handle ambiguous bases in high-throughput sequencing", "abstract": "Background: High-throughput sequencing is a powerful tool that is extensively applied in biological studies. However, sequencers may produce low-quality bases, leading to ambiguous bases, ‘N’s. PCR duplicates introduced in library preparation are conventionally removed in genomics studies, and several deduplication tools have been developed for this purpose. Two identical reads may appear different due to ambiguous bases and the existing tools cannot address ‘N’s correctly or efficiently. Results: Here we proposed and implemented TrieDedup, which uses the trie (prefix tree) data structure to compare and store sequences. TrieDedup can handle ambiguous base ‘N’s, and efficiently deduplicate at the level of raw sequences. We also reduced its memory usage by approximately 20% by implementing restrictedDict in Python. We benchmarked the performance of the algorithm and showed that TrieDedup can deduplicate reads up to 270-fold faster than pairwise comparison at a cost of 32-fold higher memory usage. Conclusions: The TrieDedup algorithm may facilitate PCR deduplication, barcode or UMI assignment, and repertoire diversity analysis of large-scale high-throughput sequencing datasets with its ultra-fast algorithm that can account for ambiguous bases due to sequencing errors.", "date": "2024-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Hu J." }, { "name": "Luo S." }, { "name": "Tian M." }, { "name": "Ye A.Y." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Adam Yongxin Ye", "email": "yeyx2626@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Jianqiao Hu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-06-18T12:44:34.691271Z", "lastUpdate": "2024-06-18T12:44:34.694901Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "AACompIdent", "description": "Protein identification by amino acid composition, and optionally pI, Mw, species, UniProtKB keyword and calibration protein. Several constellations are available, corresponding to various amino acid analysis techniques.", "homepage": "https://web.expasy.org/aacompident", "biotoolsID": "aacompident", "biotoolsCURIE": "biotools:aacompident", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://web.expasy.org/aacompident/aacomp-doc.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": null, "pmid": "9636313", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "From proteins to proteomes: Large scale protein identification by two-dimensional electrophoresis and amino acid analysis", "abstract": "Separation and identification of proteins by two-dimensional (2-D) electrophoresis can be used for protein-based gene expression analysis. In this report single protein spots, from polyvinylidene difluoride blots of micropreparative E. coli 2-D gels, were rapidly and economically identified by matching their amino acid composition, estimated pI and molecular weight against all E. coli entries in the SWISS-PROT database. Thirty proteins from an E. coli 2-D map were analyzed and identities assigned. Three of the proteins were unknown. By protein sequencing analysis, 20 of the 27 proteins were correctly identified. Importantly, correct identifications showed unambiguous “correct” score patterns. While incorrect protein identifications also showed distinctive score patterns, indicating that protein must be identified by other means. These techniques allow large-scale screening of the protein complement of simple organisms, or tissues in normal and disease states. The computer program described here is accessible via the World Wide Web at URL address (http://expasy.hcuge.ch/). © 1996 Nature Publishing Group.", "date": "1996-01-01T00:00:00Z", "citationCount": 689, "authors": [ { "name": "Wilkins M.R." }, { "name": "Pasquali C." }, { "name": "Appel R.D." }, { "name": "Ou K." }, { "name": "Golaz O." }, { "name": "Sanchez J.-C." }, { "name": "Yan J.X." }, { "name": "Gooley A.A." }, { "name": "Hughes G." }, { "name": "Humphery-Smith I." }, { "name": "Williams K.L." }, { "name": "Hochstrasser D.F." } ], "journal": "Bio/Technology" } } ], "credit": [ { "name": "ExPASy helpdesk", "email": null, "url": "https://www.expasy.org/support", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "admin", "additionDate": "2017-12-06T18:14:19Z", "lastUpdate": "2024-05-16T14:10:31.539361Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "sduvaud" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Infernal cmscan (EBI)", "description": "Infernal (\"INFERence of RNA ALignment\") is for searching DNA sequence databases (e.g. Rfam) for RNA structure and sequence similarities.", "homepage": "https://www.ebi.ac.uk/jdispatcher/rna/infernal_cmscan", "biotoolsID": "infernal_cmscan", "biotoolsCURIE": "biotools:infernal_cmscan", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "infernal", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "EBI Tools", "Job Dispatcher Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "http://eddylab.org/infernal/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.ebi.ac.uk/jdispatcher/help", "type": [ "General" ], "note": null }, { "url": "http://eddylab.org/infernal/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btt509", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Infernal 1.1: 100-fold faster RNA homology searches", "abstract": "Summary: Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input. Infernal uses CMs to search for new family members in sequence databases and to create potentially large multiple sequence alignments. Version 1.1 of Infernal introduces a new filter pipeline for RNA homology search based on accelerated profile hidden Markov model (HMM) methods and HMM-banded CM alignment methods. This enables ∼100-fold acceleration over the previous version and ∼10 000-fold acceleration over exhaustive non-filtered CM searches. © The Author 2013. Published by Oxford University Press. All rights reserved.", "date": "2013-11-15T00:00:00Z", "citationCount": 1788, "authors": [ { "name": "Nawrocki E.P." }, { "name": "Eddy S.R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/nar/gkae241", "pmid": "38597606", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.", "date": "2022-07-05T00:00:00Z", "citationCount": 867, "authors": [ { "name": "Madeira F." }, { "name": "Pearce M." }, { "name": "Tivey A.R.N." }, { "name": "Basutkar P." }, { "name": "Lee J." }, { "name": "Edbali O." }, { "name": "Madhusoodanan N." }, { "name": "Kolesnikov A." }, { "name": "Lopez R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Sean Eddy", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Job Dispatcher", "email": null, "url": "http://www.ebi.ac.uk/jdispatcher", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "jdispatcher", "additionDate": "2015-08-03T09:35:17Z", "lastUpdate": "2024-05-16T13:09:51.619759Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RADAR (EBI)", "description": "Identify gapped approximate repeats and complex repeat architectures involving many different types of repeats.", "homepage": "https://www.ebi.ac.uk/jdispatcher/pfa/radar", "biotoolsID": "radar", "biotoolsCURIE": "biotools:radar", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0237", "term": "Repeat sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0157", "term": "Sequence composition, complexity and repeats" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "EBI Tools", "Job Dispatcher Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "https://sourceforge.net/projects/repeatradar/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.ebi.ac.uk/jdispatcher/help", "type": [ "General" ], "note": null }, { "url": "https://sourceforge.net/projects/repeatradar/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/1097-0134(20001101)41:2<224::aid-prot70>3.0.co;2-z", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkae241", "pmid": "38597606", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.", "date": "2022-07-05T00:00:00Z", "citationCount": 867, "authors": [ { "name": "Madeira F." }, { "name": "Pearce M." }, { "name": "Tivey A.R.N." }, { "name": "Basutkar P." }, { "name": "Lee J." }, { "name": "Edbali O." }, { "name": "Madhusoodanan N." }, { "name": "Kolesnikov A." }, { "name": "Lopez R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Andreas Heger", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Job Dispatcher", "email": null, "url": "https://www.ebi.ac.uk/jdispatcher", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "jdispatcher", "additionDate": "2015-01-29T15:47:44Z", "lastUpdate": "2024-05-16T13:08:04.584403Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PfamScan (EBI)", "description": "PfamScan is used to search a FASTA sequence against a library of Pfam HMM.", "homepage": "https://www.ebi.ac.uk/jdispatcher/pfa/pfamscan", "biotoolsID": "pfamscan_ebi", "biotoolsCURIE": "biotools:pfamscan_ebi", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1364", "term": "Hidden Markov model" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0858", "term": "Sequence signature matches" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [ "EBI Tools", "Job Dispatcher Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.ebi.ac.uk/jdispatcher/help", "type": [ "General" ], "note": null }, { "url": "http://xfam.org/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2105-8-298", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Predicting active site residue annotations in the Pfam database", "abstract": "Background: Approximately 5% of Pfam families are enzymatic, but only a small fraction of the sequences within these families (<0.5%) have had the residues responsible for catalysis determined. To increase the active site annotations in the Pfam database, we have developed a strict set of rules, chosen to reduce the rate of false positives, which enable the transfer of experimentally determined active site residue data to other sequences within the same Pfam family. Description: We have created a large database of predicted active site residues. On comparing our active site predictions to those found in UniProtKB, Catalytic Site Atlas, PROSITE and MEROPS we find that we make many novel predictions. On investigating the small subset of predictions made by these databases that are not predicted by us, we found these sequences did not meet our strict criteria for prediction. We assessed the sensitivity and specificity of our methodology and estimate that only 3% of our predicted sequences are false positives. Conclusion: We have predicted 606110 active site residues, of which 94% are not found in UniProtKB, and have increased the active site annotations in Pfam by more than 200 fold. Although implemented for Pfam, the tool we have developed for transferring the data can be applied to any alignment with associated experimental active site data and is available for download. Our active site predictions are re-calculated at each Pfam release to ensure they are comprehensive and up to date. They provide one of the largest available databases of active site annotation. © 2007 Mistry et al; licensee BioMed Central Ltd.", "date": "2007-08-09T00:00:00Z", "citationCount": 164, "authors": [ { "name": "Mistry J." }, { "name": "Bateman A." }, { "name": "Finn R.D." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1093/nar/gkae241", "pmid": "38597606", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.", "date": "2022-07-05T00:00:00Z", "citationCount": 867, "authors": [ { "name": "Madeira F." }, { "name": "Pearce M." }, { "name": "Tivey A.R.N." }, { "name": "Basutkar P." }, { "name": "Lee J." }, { "name": "Edbali O." }, { "name": "Madhusoodanan N." }, { "name": "Kolesnikov A." }, { "name": "Lopez R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Rob Finn", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Job Dispatcher", "email": null, "url": "https://www.ebi.ac.uk/jdispatcher", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "jdispatcher", "additionDate": "2022-11-03T15:52:46.162749Z", "lastUpdate": "2024-05-16T13:01:35.233347Z", "editPermission": { "type": "group", "authors": [ "nandana" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "T-Coffee (EBI)", "description": "Multiple sequence alignment that combines several alignment methods.", "homepage": "https://www.ebi.ac.uk/jdispatcher/msa/tcoffee/", "biotoolsID": "TCoffee_EBI", "biotoolsCURIE": "biotools:TCoffee_EBI", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "tcoffee", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "T-Coffee", "EBI Tools", "Job Dispatcher Tools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "https://tcoffee.org/Projects/tcoffee/index.html", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.ebi.ac.uk/jdispatcher/help", "type": [ "General" ], "note": null }, { "url": "https://tcoffee.org/Projects/tcoffee/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1006/jmbi.2000.4042", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "T-coffee: A novel method for fast and accurate multiple sequence alignment", "abstract": "We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives. The method is broadly based on the popular progressive approach to multiple alignment but avoids the most serious pitfalls caused by the greedy nature of this algorithm. With T-Coffee we pre-process a data set of all pair-wise alignments between the sequences. This provides us with a library of alignment information that can be used to guide the progressive alignment. Intermediate alignments are then based not only on the sequences to be aligned next but also on how all of the sequences align with each other. This alignment information can be derived from heterogeneous sources such as a mixture of alignment programs and/or structure superposition. Here, we illustrate the power of the approach by using a combination of local and global pair-wise alignments to generate the library. The resulting alignments are significantly more reliable, as determined by comparison with a set of 141 test cases, than any of the popular alternatives that we tried. The improvement, especially clear with the more difficult test cases, is always visible, regardless of the phylogenetic spread of the sequences in the tests. (C) 2000 Academic Press.", "date": "2000-09-08T00:00:00Z", "citationCount": 5714, "authors": [ { "name": "Notredame C." }, { "name": "Higgins D.G." }, { "name": "Heringa J." } ], "journal": "Journal of Molecular Biology" } }, { "doi": "10.1093/nar/gkae241", "pmid": "38597606", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.", "date": "2022-07-05T00:00:00Z", "citationCount": 867, "authors": [ { "name": "Madeira F." }, { "name": "Pearce M." }, { "name": "Tivey A.R.N." }, { "name": "Basutkar P." }, { "name": "Lee J." }, { "name": "Edbali O." }, { "name": "Madhusoodanan N." }, { "name": "Kolesnikov A." }, { "name": "Lopez R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Cedric Notredame", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "CRG", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Job Dispatcher", "email": null, "url": "https://www.ebi.ac.uk/jdispatcher", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "jdispatcher", "additionDate": "2015-01-29T15:47:33Z", "lastUpdate": "2024-05-16T11:40:53.572187Z", "editPermission": { "type": "group", "authors": [ "nandana", "biomadeira" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MegaSSR", "description": "Web server for large scale microsatellite identification, classification, and marker development.", "homepage": "https://bioinformatics.um6p.ma/MegaSSR", "biotoolsID": "megassr", "biotoolsCURIE": "biotools:megassr", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0308", "term": "PCR primer design" }, { "uri": "http://edamontology.org/operation_0237", "term": "Repeat sequence analysis" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_0632", "term": "Probes and primers" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.3389/fpls.2023.1219055", "pmid": "38162302", "pmcid": "PMC10757629", "type": [], "version": null, "note": null, "metadata": { "title": "MegaSSR: a web server for large scale microsatellite identification, classification, and marker development", "abstract": "Next-generation sequencing technologies have opened new avenues for using genomic data to study and develop molecular markers and improve genetic resources. Simple Sequence Repeats (SSRs) as genetic markers are increasingly used in molecular diversity and molecular breeding programs that require bioinformatics pipelines to analyze the large amounts of data. Therefore, there is an ongoing need for online tools that provide computational resources with minimal effort and maximum efficiency, including automated development of SSR markers. These tools should be flexible, customizable, and able to handle the ever-increasing amount of genomic data. Here we introduce MegaSSR (https://bioinformatics.um6p.ma/MegaSSR), a web server and a standalone pipeline that enables the design of SSR markers in any target genome. MegaSSR allows users to design targeted PCR-based primers for their selected SSR repeats and includes multiple tools that initiate computational pipelines for SSR mining, classification, comparisons, PCR primer design, in silico PCR validation, and statistical visualization. MegaSSR results can be accessed, searched, downloaded, and visualized with user-friendly web-based tools. These tools provide graphs and tables showing various aspects of SSR markers and corresponding PCR primers. MegaSSR will accelerate ongoing research in plant species and assist breeding programs in their efforts to improve current genomic resources.", "date": "2023-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Mokhtar M.M." }, { "name": "Alsamman A.M." }, { "name": "El Allali A." } ], "journal": "Frontiers in Plant Science" } } ], "credit": [ { "name": "Morad M. Mokhtar", "email": "morad.mokhtar@ageri.sci.eg", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Achraf El Allali", "email": "achraf.elallali@um6p.ma", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-14T12:29:26.034781Z", "lastUpdate": "2024-05-14T12:29:26.037185Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "SynLinker", "description": "An integrated system to provide suitable linker candidates for novel recombinant fusion proteins.", "homepage": "http://synlinker.syncti.org/", "biotoolsID": "synlinker", "biotoolsCURIE": "biotools:synlinker", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0108", "term": "Protein expression" }, { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/synlinker-designing-linkers-and-synthetic-fusion-proteins.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://synlinker.syncti.org/help.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": null, "pmid": "26227144", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "SynLinker: An integrated system for designing linkers and synthetic fusion proteins", "abstract": "Summary: Synthetic fusion proteins have shown great potential in various biotechnological and (bio)pharmaceutical applications. They usually contain more than two protein domains joined by a linker peptide sequence which is often selected intuitively or in ad hoc manner. Thus, we developed an integrated web-based system, SynLinker, to provide appropriate linker candidates for constructing fusion proteins. We compiled a total of 2260 linker sequences comprising of natural linkers extracted from a set of non-redundant multi-domain proteins in Protein Data Bank and artificial/empirical linkers collected from literature and patents. Multiple query interface allows users to search for the desired linker candidates based on selection criteria and their preferences. In addition, a selected linker can be combined with two domain structures which are uploaded and appended at its N and C terminals, thereby predicting a de novo structure of the fusion protein. Hence, SynLinker can serve as a systematic tool for researchers who are interested in designing synthetic fusion proteins. Availability and implementation: SynLinker is freely available at http://bioinfo.bti.a-star.edu.sg/synlinker.", "date": "2015-05-25T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Liu C." }, { "name": "Chin J.X." }, { "name": "Lee D.-Y." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": null, "email": "lee_dong_yup@bti.a-star.edu.sg", "url": "http://synlinker.syncti.org/contact.php", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "Wting", "additionDate": "2017-08-03T19:02:22Z", "lastUpdate": "2024-03-26T13:47:36.513667Z", "editPermission": { "type": "public", "authors": [ "Wting" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "COVIDep", "description": "COVIDep provides an up-to-date set of B-cell and T-cell epitopes that can serve as potential vaccine targets for SARS-CoV-2. 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