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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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UMD-BRCA1/ BRCA2 databases Resource Report Resource Website 10+ mentions |
UMD-BRCA1/ BRCA2 databases (RRID:SCR_006128) | UMD-BRCA1/ BRCA2 databases | data or information resource, data repository, database, service resource, storage service resource | The UMD-BRCA1/BRCA2 databases have been set up in a joined national effort through the network of 16 diagnostic laboratories to provide up-to-date information about mutations of the BRCA1 and BRCA2 genes identified in patients with breast and/or ovarian cancer. These databases currently contain published and unpublished information about the BRCA1/BRCA2 mutations reported in French diagnostic laboratories. This database includes 28 references and 5530 mutations (1440 different mutations and 786 protein variants) The databases of BRCA1 and BRCA2 mutations were built using the Universal Mutation Database tool. For each mutation, information is provided at several levels: * at the gene level: exon and codon number, wild type and mutant codon, mutation event, mutation name and, * at the protein level: wild type and mutant amino acid, binding domain, affected domain. If you want to submit a mutation, please contact R. Lidereau., S. Caputo. or E. Rouleau. | cancer, gene, mutation, exon, codon, wild type, mutant, mutation, protein, amino acid, binding domain, affected domain, brca1, brca2, variant, polymorphism, unclassified variant, unknown variant, female, woman, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: National Institute of Health and Medical Research; Rennes; France |
Breast cancer, Ovarian cancer | French National Cancer Institute ; European Union FP7/2007-2013; Association dAide a la Recherche Cancerologique de Saint Cloud |
PMID:22144684 | The UMD- BRCA1 Locus Specific Databases constitute the intellectual property of the curators of the database. Any unauthorized copying, Storage or distribution of this material without written permission from the curators would lead to copyright infringement with possible ensuing litigation. | biotools:brca_share, nlx_151608 | https://bio.tools/brca_share | SCR_006128 | UMD-BRCA1 mutations database, UMD-BRCA1 / BRCA2 databases, UMD-BRCA1/BRCA2 databases | 2026-09-12 12:56:35 | 26 | |||
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PRED-GPCR Resource Report Resource Website 1+ mentions |
PRED-GPCR (RRID:SCR_006196) | PRED-GPCR | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | A prediction tool for GPCR Family Classification from sequence alone based on a probabilistic method that uses family-specific profile Hidden Markov Models. The PRED-GPCR system is based on a probabilistic method that uses family specific profile HMMs in order to determine to which GPCR family a query sequence belongs or resembles. The approach proposed in this method exploits the descriptive power of profile HMMs along with an exhaustive discrimination assessment method to select only highly selective and sensitive profiles, for each family. The collection of these profiles constitutes a signature library, which is scanned, for significant matches with a given query sequence. The output report for a query sequence consists of two sections: * A ranked list of the profile HMM matches, below the selected individual motif E-value cutoff, along with their corresponding family. * A ranked list of the Combined P-values, E-values as well as the number of profiles matched for each family. To cross-evaluate your results you can browse through Swiss-Prot, Trembl, Pfam and Prosite family related entries. | g-protein coupled receptor, classification, hidden markov model, sequence, fasta, family classification, motif, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:15215415 | nlx_151741, biotools:pred-gpcr | https://bio.tools/pred-gpcr | SCR_006196 | PRED-GPCR: GPCRs Family classification from sequence alone | 2026-09-12 12:56:36 | 2 | ||||||
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MouseBook Resource Report Resource Website 10+ mentions |
MouseBook (RRID:SCR_006358) | MouseBook | biomaterial supply resource, material resource, organism supplier | Databases and portal to data and ordering mouse strains from MRC Harwell including mouse stocks in FESA (Frozen Embryo and Sperm Archive), mutants from the mutagenesis screen, the ENU DNA archive, standardized phenotyping procedures, imprinting genes and chromosome anomalies. The portal integrates curated information from the MRC Harwell stock resource, and other Harwell databases, with information from external data resources to provide added value information above and beyond what is available through other routes such as IMSR (International Mouse Stain Resource). MouseBook can be searched either using an intuitive Google-style free text search or using the Mammalian Phenotype Ontology (MP) tree structure. Text searches can be on gene, allele, strain identifier (e.g. MGI ID) or phenotype term and are assisted by automatic recognition of term types and autocompletion of gene and allele names covered by the database. Results are returned in a tabbed format providing categorized results identified from each of the catalogs in MouseBook. Individual results lines from each catalog include information on gene, allele, chromosomal location and phenotype and provide a simple click-through link to further information as well as ordering the strain. The infrastructure underlying MouseBook has been designed to be extensible, allowing additional data sources to be added enabling other sites to make their data directly available through MouseBook. | mutant mouse strain, gene, allele, phenotype, embryonic mouse, embryo, sperm, live, chromosomal location, mutant mouse line, imprint, standard operating procedure, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: bio.tools is related to: MPO |
Motor neuron disease, Chromosomal anomaly | MRC | PMID:19854936 | Public | nlx_152127, biotools:mousebook | https://bio.tools/mousebook | SCR_006358 | Mouse Book | 2026-09-12 12:56:38 | 18 | |||
|
IRanges Resource Report Resource Website 50+ mentions |
IRanges (RRID:SCR_006420) | IRanges | software resource | Software tool for computing and annotating genomic ranges.Provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent Vector API as much as possible. | Annotating genomic ranges, computing genomic ranges, genomic ranges, storing ranges of integers, bio.tools |
is used by: riboWaltz is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:23950696 | Free, Available for download, Freely available | OMICS_01163, biotools:iranges | https://bio.tools/iranges | SCR_006420 | Infrastructure for manipulating intervals on sequences | 2026-09-12 12:56:39 | 88 | |||||
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VICUNA Resource Report Resource Website 10+ mentions |
VICUNA (RRID:SCR_006302) | VICUNA | software resource | A de novo assembly program targeting populations with high mutation rates. | c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Broad Institute |
PMID:22974120 | biotools:vicuna, OMICS_02162 | https://bio.tools/vicuna | SCR_006302 | 2026-09-12 12:56:37 | 26 | |||||||
|
MSIsensor Resource Report Resource Website 100+ mentions |
MSIsensor (RRID:SCR_006418) | MSIsensor | software resource | A C++ software program for automatically detecting somatic and germline variants at microsatellite regions. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples. | c++, somatic variant, germline variant, microsatellite, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Tumor, Normal | PMID:24371154 | Copyrighted, See LICENSE | biotools:msisensor, OMICS_02192 | https://bio.tools/msisensor | SCR_006418 | 2026-09-12 12:56:39 | 168 | |||||
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TSSer Resource Report Resource Website |
TSSer (RRID:SCR_006419) | TSSer | software resource | A computational pipeline to analyze differential RNA sequencing (dRNA-seq) data to determine transcription start sites genome-wide. | differential rna sequencing, transcription start site, rna-seq, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Basel; Basel; Switzerland |
PMID:24371151 | GNU General Public License | biotools:tsser, OMICS_02191 | https://bio.tools/tsser | SCR_006419 | TSSer: a computational pipeline to identify transcription start sites in bacterial genomes | 2026-09-12 12:56:39 | 0 | |||||
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Flycircuit Resource Report Resource Website 50+ mentions |
Flycircuit (RRID:SCR_006375) | atlas, data or information resource, database, service resource, storage service resource | FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain. | drosophila, fly brain, neuron reconstruction, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Virtual Fly Brain has parent organization: National Tsing Hua University; Hsinchu; Taiwan |
PMID:21129968 | r3d100012173, nif-0000-07738, biotools:FlyCircuit | https://bio.tools/FlyCircuit, https://doi.org/10.17616/R3293N | SCR_006375 | Fly Circuit - A Database of Drosophila Brain Neurons, Fly Circuit, Flycircuit database, Fly Circuit Database, FlyCircuit - A Database of Drosophila Brain Neurons | 2026-09-12 12:56:39 | 50 | |||||||
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HUDSEN Resource Report Resource Website 1+ mentions |
HUDSEN (RRID:SCR_006324) | HUDSEN | community building portal, data or information resource, portal | Forum for researchers in human developmental biology and related fields to meet and establish links. | development, genetics, embryology, embryonic, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: eMouseAtlas is related to: aGEM has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom is parent organization of: HUDSEN Electronic Atlas of the Developing Human Brain is parent organization of: HUDSEN Human Gene Expression Spatial Database |
nlx_152025, biotools:hudsen | https://bio.tools/hudsen | SCR_006324 | Human Developmental Studies Network | 2026-09-12 12:56:38 | 5 | |||||||
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PomBase Resource Report Resource Website 100+ mentions |
PomBase (RRID:SCR_006586) | PomBase | data or information resource, database, service resource | Model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation. PomBase also provides a community hub for researchers, providing genome statistics, a community curation interface, news, events, documentation, mailing lists, and welcomes data submissions. | fission yeast, gene ontology, genome sequence, schizosaccharomyces pombe (4896), schizosaccharomyces pombe, dna, protein, cosmic assembly, intron, go, chromosome, telomere, centromere, mating region, data mapping, model organism, genome, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: AmiGO is related to: GeneDB Spombe has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: University College London; London; United Kingdom is parent organization of: Fission Yeast Phenotype Ontology is parent organization of: Pompep |
Wellcome Trust WT090548MA | PMID:22039153 | Public, Acknowledgement requested | biotools:pombase, nlx_144356, r3d100011478 | https://bio.tools/pombase, https://doi.org/10.17616/R3NS78 | http://www.sanger.ac.uk/Projects/S_pombe/ | SCR_006586 | Schizosaccharomyces pombeGenome Sequencing Project | 2026-09-12 12:56:42 | 396 | |||
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COLT-Cancer Resource Report Resource Website 10+ mentions |
COLT-Cancer (RRID:SCR_006485) | COLT-Cancer | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | The COLT-Cancer database is a collection of shRNA dropout signatures profiles, covering ~16000 human genes, and derived from more than 70 Pancreatic, Ovarian and Breast human cancer cell-lines using the microarray detection platform developed in the COLT (CCBR-OICR Lentiviral Technology) facility at the Moffat Lab. All shRNA dropout profiles are freely available through download or queries via this website. | gene, shrna profile, shrna, functional genetics, cancer, cell line, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Toronto; Ontario; Canada |
Pancreatic cancer, Ovarian cancer, Breast cancer | Ontario Institute for Cancer Research ; Terry Fox Research Institute ; Canadian Institutes of Health Research ; Canada Foundation for Innovation ; Ontario Research Fund |
PMID:22102578 | Free | biotools:colt-cancer, nlx_149426 | https://bio.tools/colt-cancer | SCR_006485 | CCBR-OICR Lentiviral Technology Cancer, COLT-Cancer database | 2026-09-12 12:56:40 | 11 | |||
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COHCAP Resource Report Resource Website 10+ mentions |
COHCAP (RRID:SCR_006499) | COHCAP | software resource | An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. | java, perl, s/r, java swing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23598999 | Acknowledgement requested, Attribution Assurance License | biotools:cohcap, OMICS_00595 | https://bio.tools/cohcap | SCR_006499 | City of Hope CpG Island Analysis Pipeline, COHCAP - City of Hope CpG Island Analysis Pipeline | 2026-09-12 12:56:41 | 19 | |||||
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Phenotypes and eXposures Toolkit Resource Report Resource Website 50+ mentions |
Phenotypes and eXposures Toolkit (RRID:SCR_006532) | PhenX Toolkit | catalog, data or information resource, data set, database, narrative resource, service resource, standard specification | Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols. | PhenX project, genome, phenotype, genome-wide association study, genetic variation, genomic study, substance abuse, addiction, substance use, environmental exposure, disease susceptibility, outcome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: RTI International has parent organization: Consensus Measures for Phenotype and Exposure has parent organization: Trans-Omics for Precision Medicine (TOPMed) Program has organization facet: PhenX Phenotypic Terms is organization facet of: Consensus Measures for Phenotype and Exposure |
NCI ; NHGRI U01 HG004597; NHGRI U24 HG012556; NHGRI U41HG007050; NHLBI ; NIDA ; NIMHD ; NIMH ; NINDS ; OBSSR ; ODP ; TRSP |
PMID:21749974 | Restricted | SCR_017475, biotools:PhenX_toolkit, nlx_144102 | https://bio.tools/PhenX_Toolkit | SCR_006532 | Phenotypes and eXposures Toolkit | 2026-09-12 12:56:41 | 73 | ||||
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FlyBase Resource Report Resource Website 1000+ mentions |
FlyBase (RRID:SCR_006549) | FB | data or information resource, data repository, database, organism-related portal, portal, service resource, storage service resource, topical portal | Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar. | RIN, Resource Information Network, mutant, gene, genome, blast, genotype, phenotype, allele, sequence, stock, image, movie, controlled term, video resource, image collection, life-cycle, genome, expression, rna-seq, genetics, drosophilidae, bio.tools, FASEB list, RRID Community Authority |
is used by: NIF Data Federation is used by: Resource Identification Portal is used by: PhenoGO is used by: Integrated Animals is used by: Drososhare 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: re3data.org is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: Resource Information Network is related to: FlyMine is related to: Virtual Fly Brain is related to: AmiGO is related to: Drosophila melanogaster Exon Database is related to: HomoloGene is related to: UniParc at the EBI is related to: UniParc is related to: Gene Ontology is related to: NIH Data Sharing Repositories is related to: GBrowse is related to: Integrated Manually Extracted Annotation is related to: PhenoGO has parent organization: Harvard University; Cambridge; United States has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: Indiana University; Indiana; USA has parent organization: University of New Mexico; New Mexico; USA is parent organization of: Drosophila anatomy and development ontologies is parent organization of: Fly Taxonomy is parent organization of: FlyBase Controlled Vocabulary is parent organization of: Drosophila Development Ontology is organization facet of: Alliance of Genome Resources |
Indiana Genomics Initiative ; MRC ; NIH Blueprint for Neuroscience Research ; NIHGRI P41 HG000739; NSF |
PMID:24234449 PMID:22127867 PMID:18948289 PMID:18641940 PMID:18160408 PMID:17099233 PMID:16381917 PMID:15608223 PMID:12519974 PMID:11752267 PMID:11465064 PMID:9847148 PMID:9399806 PMID:9045212 PMID:8594600 PMID:8578603 PMID:7937045 PMID:7925011 |
nif-0000-00558, r3d100010591, OMICS_01649, biotools:flybase | https://bio.tools/flybase, https://doi.org/10.17616/R3903Q | http://flybase.net | SCR_006549 | flybase A Drosophila Genomic and Genetic Database, FlyBase: A Database of Drosophila Genes and Genomes, FLYBASE, FlyBase: A Database of Drosophila Genes & Genomes, FB | 2026-09-12 12:56:41 | 4234 | ||||
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Kalign Resource Report Resource Website 100+ mentions |
Kalign (RRID:SCR_011810) | Kalign | software resource | A fast and accurate multiple sequence alignment algorithm. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
PMID:16343337 DOI:10.1093/bioinformatics/btz795 |
Free | OMICS_00978, biotools:kalign | https://bio.tools/kalign, https://sources.debian.org/src/kalign/ | SCR_011810 | 2026-09-12 12:57:40 | 123 | ||||||
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MAFFT Resource Report Resource Website 10000+ mentions |
MAFFT (RRID:SCR_011811) | MAFFT | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments. | alignment, amino acid, nucleotide, sequence, DNA, sequence alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
EMBL ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:12136088 PMID:17118958 PMID:16362903 PMID:15661851 PMID:18439255 PMID:23023983 DOI:10.1093/bib/bbn013 |
biotools:MAFFT, OMICS_00979 | https://www.ebi.ac.uk/Tools/msa/mafft/, https://www.genome.jp/tools-bin/mafft, https://myhits.isb-sib.ch/cgi-bin/mafft, https://bio.tools/MAFFT, https://sources.debian.org/src/mafft/ | SCR_011811 | Multiple Alignment using Fast Fourier Transform, MAFFT version 5, MAFFT version 7 | 2026-09-12 12:57:40 | 24687 | |||||
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CGView Resource Report Resource Website 100+ mentions |
CGView (RRID:SCR_011779) | CGView | software resource | A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Alberta; Alberta; Canada |
DOI:10.1093/bioinformatics/bti054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00905, biotools:cgview | https://bio.tools/cgview, https://sources.debian.org/src/cgview/ | SCR_011779 | Circular Genome Viewer | 2026-09-12 12:57:39 | 310 | |||||
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PSAR-Align Resource Report Resource Website 1+ mentions |
PSAR-Align (RRID:SCR_011814) | PSAR-Align | software resource | Software for improving multiple sequence alignment using probabilistic sampling. | c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24222208 | Free | OMICS_00987, biotools:psar | https://bio.tools/psar | SCR_011814 | PSAR-Align: improving multiple sequence alignment using probabilistic sampling | 2026-09-12 12:57:40 | 1 | |||||
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Gaggle Resource Report Resource Website |
Gaggle (RRID:SCR_011780) | Gaggle | software resource | An open source software tool for visualizing high-density data plotted against coordinates on the genome. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Open unspecified license, Free | biotools:ggb, OMICS_00909 | https://bio.tools/ggb | SCR_011780 | 2026-09-12 12:57:39 | 0 | |||||||
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PatMaN Resource Report Resource Website 50+ mentions |
PatMaN (RRID:SCR_011821) | PatMaN | software resource | Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | c++, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18467344 DOI:10.1093/bioinformatics/btn223 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00997, biotools:patman | https://bio.tools/patman, https://sources.debian.org/src/patman/ | SCR_011821 | PatMaN - A DNA pattern matcher for short sequences | 2026-09-12 12:57:40 | 61 |
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