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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BEAST Resource Report Resource Website 5000+ mentions |
BEAST (RRID:SCR_010228) | data processing software, data analysis software, software resource, software repository, sequence analysis software, software application | A cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. | bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: TempEst is related to: BEAST2 is related to: PhyDyn has parent organization: University of Edinburgh; Scotland; United Kingdom |
DOI:10.1186/1471-2148-7-214 | nlx_156859, OMICS_04233, biotools:beast, SCR_015988 | http://www.nitrc.org/projects/beast-library, https://bio.tools/beast, https://sources.debian.org/src/beast-mcmc/ | http://beast.bio.ed.ac.uk/Main_Page | SCR_010228 | BEaST Segmentation Library, Beast Software | 2026-08-04 09:42:40 | 6460 | ||||||
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WEBLOGO Resource Report Resource Website 1000+ mentions |
WEBLOGO (RRID:SCR_010236) | data access protocol, software resource, service resource, web service | Web application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator. | Generate sequence logo, pattern graphical representation, multiple sequence alignment, sequence logo generator, amino acid sequence alignment, nucleic acid sequence alignment, sequence alignment representation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
NHGRI K22 HG00056; Searle Scholars program ; NIGMS P50 GM62412 |
PMID:15173120 | Free, Available for download, Freely available | nlx_156853, biotools:weblogo_3 | http://weblogo.threeplusone.com/, https://bio.tools/weblogo_3 | SCR_010236 | WebLogo Version 2.8.2, WebLogo3, WebLogo | 2026-08-04 09:42:40 | 3653 | |||||
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Geneious Resource Report Resource Website 10000+ mentions |
Geneious (RRID:SCR_010519) | data processing software, data analysis software, data management software, software resource, sequence analysis software, software application, software toolkit | Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools. | Sequence alignment software, data management software, analysis software, Geneious Biologics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is parent organization of: Geneious Microsatellite Plugin |
PMID:22543367 | Restricted | OMICS_00016, biotools:geneious | http://nebc.nerc.ac.uk/news/geneiousonbl, https://bio.tools/geneious | SCR_010519 | Geneious Prime, Geneious 11.0, Geneious 11.1.2, Geneious 8.1, Geneious Basic | 2026-08-04 09:42:46 | 12252 | ||||||
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Pathema Resource Report Resource Website 1+ mentions |
Pathema (RRID:SCR_010585) | Pathema | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | Pathema is one of the eight Bioinformatics Resource Centers designed to serve as a core resource for the bio-defense and infectious disease research community. Pathema strives to support basic research and accelerate scientific progress for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases developed to target the specific data and analysis needs of each scientific community. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses. Pathema facilitates the scientific exploration of genomic and related data through its integration with web-based analysis tools, customized to obtain, display, and compute results relevant to ongoing pathogen research. Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genome sequencing projects and providing access to the results of inter-genomic comparisons for these organisms. The Pathema BRC contract ends in December 2009. At that time JCVI will cease maintenance of the Pathema web resource and data. The PATRIC team, located at the Virginia Bioinformatics Institute, created and maintains a consolidated BRC for all of the NIAID category A-C priority pathogenic bacteria. The EuPathDB team at the University of Pennsylvania will support all eukaryotic pathogens. Pathema transferred all data and software to PATRIC and EuPathDB for incorporation into their new Web-based bioinformatics resource. | bacillus anthracis, clostridium botulinum, burkholderia mallei, burkholderia pseudomallei, clostridium perfringens, entamoeba histolytica, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: J. Craig Venter Institute |
NIAID contract HHSN266200400038C | PMID:19843611 | biotools:pathema, nlx_45829 | https://bio.tools/pathema | SCR_010585 | Pathema Genome Resource, Pathema Bioinformatics Resource Center | 2026-08-04 09:42:43 | 6 | |||||
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LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data processing software, software application, software resource, data analysis software | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool, https://bio.tools/limma, https://sources.debian.org/src/r-bioc-limma/ | SCR_010943 | Linear Models for Microarray Data | 2026-08-04 09:42:49 | 24583 | ||||||
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MutPred Resource Report Resource Website 100+ mentions |
MutPred (RRID:SCR_010778) | MutPred | web application, software resource | Web application tool developed to classify an amino acid substitution as disease-associated or neutral in human. | bio.tools |
is used by: HmtVar is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Indiana University; Indiana; USA |
biotools:mutpred, OMICS_00154 | https://bio.tools/mutpred | SCR_010778 | 2026-08-04 09:42:47 | 409 | ||||||||
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ArrayAnalysis.org Resource Report Resource Website 50+ mentions |
ArrayAnalysis.org (RRID:SCR_010932) | ArrayAnalysis.org | data analysis service, analysis service resource, software resource, production service resource, service resource | Tools for microarray quality control and pre-processing. | r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23620278 | Acknowledgement requested | OMICS_00742, biotools:arrayanalysis.org | https://bio.tools/arrayanalysis.org | SCR_010932 | ArrayAnalysis | 2026-08-04 09:42:48 | 72 | |||||
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nsSNPAnalyzer Resource Report Resource Website 10+ mentions |
nsSNPAnalyzer (RRID:SCR_010780) | nsSNPAnalyzer | data analysis service, data processing software, data analysis software, analysis service resource, software resource, software application, production service resource, service resource | A tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a phenotypic effect. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
OMICS_00156, biotools:nssnpanalyzer | https://bio.tools/nssnpanalyzer | SCR_010780 | nsSNPAnalyzer: predicting disease-associated nonsynonymous single nucleotide polymorphisms | 2026-08-04 09:42:49 | 46 | |||||||
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icy Resource Report Resource Website 100+ mentions |
icy (RRID:SCR_010587) | ICY | data processing software, source code, software development tool, software resource, software repository, software application, image processing software, image analysis software, service resource, software development environment | An open community platform for bioimage informatics providing the software resources to visualize, annotate and quantify bioimaging data. To bridge the gap between developers and users, it combines: a) an open-source image analysis software, offering a powerful and flexible environment for developers such as applied mathematicians to write algorithms fast and efficiently; b) a common set of tools to view and manipulate data, and a set of plugins to perform specific quantification or analysis on images; c) a community-based website centralizing all plugins and resources to facilitate their management and maximize their visibility towards users. Workspaces are virtual groups of plugins dedicated to a specific application or image processing domain. By downloading a workspace, ICY automatically installs all corresponding plugins. The workspaces are enabled, but the editing section is not ready yet. If you want to publish a plugin on this website, its code has to be GPL. Source code is available and provided in each application download. | image analysis, microscopy, javascript, python, plugin, protocol, script, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Pasteur Institute |
Centre National de la Recherche Scientifique ; French National Research Agency ANR-10-INBS-04-06 |
PMID:22743774 | Free, Open unspecified license, GNU General Public License, v3, The community can contribute to this resource | biotools:icy, nlx_45928 | https://bio.tools/icy | SCR_010587 | icy bioimage analysis | 2026-08-04 09:42:44 | 320 | ||||
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Velvet Resource Report Resource Website 1000+ mentions |
Velvet (RRID:SCR_010755) | Velvet | data processing software, data analysis software, software resource, sequence analysis software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | de novo, genomic, assembly, short, read, sequencing, de Bruijn, graph, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Velvet-SC is related to: shovill has parent organization: European Bioinformatics Institute |
EMBL | PMID:18349386 DOI:10.1101/gr.074492.107 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00038, biotools:velvet | https://www.ebi.ac.uk/~zerbino/velvet/, https://bio.tools/velvet, https://sources.debian.org/src/velvet/ | SCR_010755 | 2026-08-04 09:42:46 | 1036 | |||||
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BWA Resource Report Resource Website 1000+ mentions |
BWA (RRID:SCR_010910) | BWA | data processing software, alignment software, data analysis software, software resource, sequence analysis software, software application, image analysis software | Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp. | sequence, alignment, reference, genome, human, short, long, read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill is related to: Proovread is related to: BWA-MEM2 has parent organization: SourceForge is required by: RelocaTE |
PMID:19451168 PMID:20080505 DOI:10.1093/bioinformatics/btp324 |
Free, Available for download, Freely available | SCR_015853, biotools:bwa-sw, OMICS_00654 | https://sourceforge.net/projects/bio-bwa/files/, https://bio.tools/bwa-sw, https://sources.debian.org/src/bwa/ | SCR_010910 | Burrows-Wheeler Aligner (BWA), Burrows-Wheeler Aligner | 2026-08-04 09:42:48 | 2291 | |||||
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GWAMA Resource Report Resource Website 100+ mentions |
GWAMA (RRID:SCR_006624) | GWAMA | data processing software, software application, software resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for meta analysis of whole genome association data. | meta, analysis, genome, association, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Centre for Human Genetics |
PMID:20509871 DOI:10.1186/1471-2105-11-288 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gwama, OMICS_00235 | https://bio.tools/gwama, https://sources.debian.org/src/gwama/ | http://www.well.ox.ac.uk/GWAMA/ | SCR_006624 | Genome-Wide Association Meta Analysis | 2026-08-04 09:41:38 | 175 | ||||
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Immune Epitope Database and Analysis Resource (IEDB) Resource Report Resource Website 100+ mentions |
Immune Epitope Database and Analysis Resource (IEDB) (RRID:SCR_006604) | IEDB | data analysis service, analysis service resource, storage service resource, data repository, production service resource, service resource | Repository contains antibody/B cell and T cell epitope information and epitope prediction and analysis tools. Immune epitopes are defined as molecular structures recognized by specific antigen receptors of the immune system, namely antibodies, B cell receptors, and T cell receptors. Immune epitopes from infectious diseases, excluding HIV, and immune-mediated diseases and the accompanying biological information are included. | human, non-human primate, rodent, pig, cat, non-human animal, t cell, b cell, epitope, infectious disease, major histocompatibility complex, bio.tools, FASEB list |
is listed by: NIH Data Sharing Repositories is listed by: Debian is listed by: bio.tools is affiliated with: AIRR Knowledge Commons has parent organization: NIAID has organization facet: La Jolla Institute for Immunology |
niad | PMID:39558162 | open | nif-0000-03017, biotools:iedb, r3d100012702 | https://nextgen-tools.iedb.org/, https://doi.org/10.17616/R3X217 | SCR_006604 | Immune Epitope Database and Analysis Resource, , IEDB | 2026-08-04 09:41:38 | 383 | ||||
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Phytozome Resource Report Resource Website 1000+ mentions |
Phytozome (RRID:SCR_006507) | Phytozome | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | A comparative platform for green plant genomics. Families of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology / paralogy relationships as well as clade specific genes and gene expansions. As of release v9.1, Phytozome provides access to forty-one sequenced and annotated green plant genomes which have been clustered into gene families at 20 evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genome, genomics, plant, green plant, cluster sequence, alignment, gene, node, cluster, blast, blat, biomart, peptide homolog, gene ancestry, sequence, annotation, gene structure, gene family, genome organization, comparative genomics, physiology, comparative, bio.tools, FASEB list |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: Plant Co-expression Annotation Resource has parent organization: DOE Joint Genome Institute has parent organization: Lawrence Berkeley National Laboratory |
Gordon and Betty Moore Foundation ; DOE DE-AC02-05CH11231 |
PMID:22110026 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:phytozome, nlx_151490, r3d100010850 | https://bio.tools/phytozome, https://doi.org/10.17616/R38021 | SCR_006507 | 2026-08-04 09:41:36 | 3108 | |||||
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Gene Expression Database Resource Report Resource Website 50+ mentions |
Gene Expression Database (RRID:SCR_006539) | GXD | storage service resource, data repository, service resource, database, data or information resource | Community database that collects and integrates the gene expression information in MGI with a primary emphasis on endogenous gene expression during mouse development. The data in GXD are obtained from the literature, from individual laboratories, and from large-scale data providers. All data are annotated and reviewed by GXD curators. GXD stores and integrates different types of expression data (RNA in situ hybridization; Immunohistochemistry; in situ reporter (knock in); RT-PCR; Northern and Western blots; and RNase and Nuclease s1 protection assays) and makes these data freely available in formats appropriate for comprehensive analysis. There is particular emphasis on endogenous gene expression during mouse development. GXD also maintains an index of the literature examining gene expression in the embryonic mouse. It is comprehensive and up-to-date, containing all pertinent journal articles from 1993 to the present and articles from major developmental journals from 1990 to the present. GXD stores primary data from different types of expression assays and by integrating these data, as data accumulate, GXD provides increasingly complete information about the expression profiles of transcripts and proteins in different mouse strains and mutants. GXD describes expression patterns using an extensive, hierarchically-structured dictionary of anatomical terms. In this way, expression results from assays with differing spatial resolution are recorded in a standardized and integrated manner and expression patterns can be queried at different levels of detail. The records are complemented with digitized images of the original expression data. The Anatomical Dictionary for Mouse Development has been developed by our Edinburgh colleagues, as part of the joint Mouse Gene Expression Information Resource project. GXD places the gene expression data in the larger biological context by establishing and maintaining interconnections with many other resources. Integration with MGD enables a combined analysis of genotype, sequence, expression, and phenotype data. Links to PubMed, Online Mendelian Inheritance in Man (OMIM), sequence databases, and databases from other species further enhance the utility of GXD. GXD accepts both published and unpublished data. | endogenous, expression assay, expression data, expression image, gene expression, genes, image, immunohistochemistry, in situ reporter, knock in, mouse, mouse mutant, northern blot, nuclease protection assay, rna in situ hybridization, rnase protection assay, rt-pcr, western blot, endogenous gene expression, mouse development, gene, transcript, protein, annotation, development, embryonic mouse, bio.tools, FASEB list |
is listed by: GUDMAP Ontology is listed by: NIDDK Information Network (dkNET) is listed by: Debian is listed by: bio.tools is related to: VisiGene Image Browser is related to: Mouse Genome Informatics (MGI) is related to: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project is related to: EMAGE Gene Expression Database is related to: aGEM has parent organization: Jackson Laboratory is parent organization of: Adult Mouse Anatomy Ontology is parent organization of: Mouse Anatomical Dictionary Browser |
NICHD HD033745 | PMID:21062809 | Free | nif-0000-01253, biotools:gxd, SCR_017529 | https://bio.tools/gxd | SCR_006539 | Jackson Lab Gene Expression Database | 2026-08-04 09:41:38 | 56 | ||||
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MIRIAM Resources Resource Report Resource Website 1+ mentions |
MIRIAM Resources (RRID:SCR_006697) | web service, software resource, catalog, data access protocol, narrative resource, standard specification, database, data or information resource | A set of online services created in support of MIRIAM, a set of guidelines for the annotation and curation of computational models. The core of MIRIAM Resources is a catalogue of data types (namespaces corresponding to controlled vocabularies or databases), their URIs and the corresponding physical URLs or resources. Access to this data is made available via exports (XML) and Web Services (SOAP). MIRIAM Resources are developed and maintained under the BioModels.net initiative, and are free for use by all. MIRIAM Resources are composed of four components: a database, some Web Services, a Java library and this web application. * Database: The core of the system is a MySQL database. It allows us to store the data types (which can be controlled vocabularies or databases), their URIs and the corresponding physical URLs, and other details such as documentation and resource identifier patterns. Each entry contains a diverse set of details about the data type: official name and synonyms, root URI, pattern of identifiers, documentation, etc. Moreover, each data type can be associated with several resources (or physical locations). * Web Services: Programmatic access to the data is available via Web Services (based on Apache Axis and SOAP messages). In addition, REST-based services are currently being developed. This API allows one to not only resolve model annotations, but also to generate appropriate URIs, based upon the provision of a resource name and accession number. A list of available web services, and a WSDL are provided. A browser-based online demonstration of the Web Services is also available to try. * Java Library: A Java library is provided to access the Web Services. The documentation explains where to download it, its dependencies, and how to use it. * Web Application: A Web application, using an Apache Tomcat server, offers access to the whole data set via a Web browser. It is possible to browse by data type names as well as browse by tags. A search engine is also provided. | life science, bio.tools |
is used by: Identifiers.org is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:22140103 PMID:18078503 |
Free | nlx_69582, biotools:miriam | https://bio.tools/miriam | SCR_006697 | MIRIAM Registry | 2026-08-04 09:41:41 | 1 | ||||||
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PeptideAtlas Resource Report Resource Website 100+ mentions |
PeptideAtlas (RRID:SCR_006783) | PeptideAtlas | storage service resource, data repository, service resource, database, data or information resource | Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database. | proteomics, peptide, mass spectrometry, annotation, eukaryotic, genome, peptide sequence, high-throughput mass spectrometry, ensembl, peptideprophet, protein sequence, blood plasma, protein, eukaryotic cell, dna, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: ProteomeXchange is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: ProteomeXchange is related to: NIH Data Sharing Repositories is related to: Integrated Manually Extracted Annotation has parent organization: Institute for Systems Biology; Washington; USA |
NCI ; NHGRI ; NIGMS |
PMID:20013378 PMID:23215161 PMID:16381952 PMID:15642101 |
Public, The community can contribute to this resource, Acknowledgement requested | nif-0000-03266, r3d100010889, biotools:peptideatlas | https://bio.tools/peptideatlas, https://doi.org/10.17616/R3BK61 | SCR_006783 | Peptide Atlas, PeptideAtlas | 2026-08-04 09:41:42 | 479 | ||||
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Descriptions of Plant Viruses Resource Report Resource Website 10+ mentions |
Descriptions of Plant Viruses (RRID:SCR_006656) | topical portal, portal, database, data or information resource | DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene. For comparative purposes, it also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA genome. The start and end positions of each feature (gene, non-translated region and the like) have been recorded and checked for accuracy. As far as possible, nomenclature for genes and proteins are standardized within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the website in FASTA format. The sequence information can also be accessed via client software for PC computers (freely downloadable from the website) that enable users to make an easy selection of sequences and features of a chosen virus for further analyses. The public sequence databases contain vast amounts of data on virus genomes but accessing and comparing the data, except for relatively small sets of related viruses can be very time consuming. The procedure is made difficult because some of the sequences on these databases are incorrectly named, poorly annotated or redundant. The NCBI Reference Sequence project (1) provides a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA) and protein products, for major research organisms. This now includes curated information for a single sequence of each fully sequenced virus species. While this is a welcome development, it can only deal with complete sequences. An important feature of DPV is the opportunity to access genes (and other features) of multiple sequences quickly and accurately. Thus, for example, it is easy to obtain the nucleotide or amino acid sequences of all the available accessions of the coat protein gene of a given virus species or for a group of viruses. To increase its usefulness further, DPVweb also contains a single representative sequence of all other fully sequenced virus species with an RNA or single-stranded DNA (ssDNA) genome. Sponsors: This site is supported by the Association of Applied Biologists and the Zhejiang Academy of Agricultural Sciences, Hangzhou, People''s Republic of China. | family, fungi, gene, amino acid, comparative, development, dna, genome, genomic, genus, nomenclature, non-translated, nucleotide, organism, plant, product, protein, protozoa, region, rna, satellite, sequence, single, specie, taxonomic, transcript, viral databases, viroid, virus, bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-21127, biotools:dpvweb | https://bio.tools/dpvweb | SCR_006656 | DPV | 2026-08-04 09:41:40 | 11 | ||||||||
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Ensembl Genomes Resource Report Resource Website 100+ mentions |
Ensembl Genomes (RRID:SCR_006773) | web service, software resource, data access protocol, database, data or information resource | Database portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualization platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community - essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimized data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualized in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site. | genome, gold standard, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: Ensembl is related to: g:Profiler has parent organization: European Bioinformatics Institute |
European Molecular Biology Laboratory ; European Union FELICS 021902 (RII3); BBSRC BB/F019793/1 |
PMID:24163254 PMID:19884133 |
r3d100011197, OMICS_01648, nlx_65207, biotools:ensembl_genomes | https://bio.tools/ensembl_genomes, https://doi.org/10.17616/R3MW6M | SCR_006773 | Ensembl Genomes: Extending Ensembl across the taxonomic space, EnsemblGenomes, Ensembl Genome | 2026-08-04 09:41:42 | 276 | ||||||
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canSAR Resource Report Resource Website 50+ mentions |
canSAR (RRID:SCR_006794) | canSAR | data analysis service, analysis service resource, production service resource, service resource, database, data or information resource | canSAR is an integrated database that brings together biological, chemical, pharmacological (and eventually clinical) data. Its goal is to integrate this data and make it accessible to cancer research scientists from multiple disciplines, in order to help with hypothesis generation in cancer research and support translational research. This cancer research and drug discovery resource was developed to utilize the growing publicly available biological annotation, chemical screening, RNA interference screening, expression, amplification and 3D structural data. Scientists can, in a single place, rapidly identify biological annotation of a target, its structural characterization, expression levels and protein interaction data, as well as suitable cell lines for experiments, potential tool compounds and similarity to known drug targets. canSAR has, from the outset, been completely use-case driven which has dramatically influenced the design of the back-end and the functionality provided through the interfaces. The Web interface provides flexible, multipoint entry into canSAR. This allows easy access to the multidisciplinary data within, including target and compound synopses, bioactivity views and expert tools for chemogenomic, expression and protein interaction network data. | molecular target, expression, cell line, compound, molecule, protein, structure, ligand, drug, 3d, genomics, 3d complex, bioactivity, protein affinity, cell line sensitivity, pathway, annotation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: BindingDB is related to: Gene Ontology has parent organization: Cancer Research UK |
Cancer | Cancer Research UK C309/A8274 | PMID:22013161 | CanSAR is freely available to all cancer researchers. By using canSAR you are agreeing to the Terms of Use, Https://cansar.icr.ac.uk/cansar/terms-of-use/ | biotools:cansar, nlx_149410 | https://bio.tools/cansar | SCR_006794 | 2026-08-04 09:41:42 | 54 |
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