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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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IPD - Immuno Polymorphism Database Resource Report Resource Website 10+ mentions |
IPD - Immuno Polymorphism Database (RRID:SCR_003004) | IPD | database, data or information resource | A set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: * IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, * IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; * IPD-human platelet antigens, alloantigens expressed only on platelets and * IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterized melanoma cell lines. | polymorphic gene, immune system, gene, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
European Union contract QLRI-CT-200!-01325; NCI P01 111412 |
PMID:19875415 PMID:18449992 PMID:15608253 |
biotools:ipd, nif-0000-03038, r3d100010797 | https://bio.tools/ipd, https://doi.org/10.17616/R3KK7K | SCR_003004 | IPD-The Immuno Polymorphism Database, IPD - The Immuno Polymorphism Database | 2026-08-06 09:25:46 | 24 | |||||
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ResponseNet Resource Report Resource Website 1+ mentions |
ResponseNet (RRID:SCR_003176) | ResponseNet | data analysis service, production service resource, analysis service resource, service resource | WebServer that identifies high-probability signaling and regulatory paths that connect input data sets. The input includes two weighted lists of condition-related proteins and genes, such as a set of disease-associated proteins and a set of differentially expressed disease genes, and a molecular interaction network (i.e., interactome). The output is a sparse, high-probability interactome sub-network connecting the two sets that is biased toward signaling pathways. This sub-network exposes additional proteins that are potentially involved in the studied condition and their likely modes of action. Computationally, it is formulated as a minimum-cost flow optimization problem that is solved using linear programming. | interactome, gene, protein, signaling pathway, signaling, regulatory, pathway, regulatory pathway, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel |
PMID:23761447 PMID:21576238 |
Free, Freely available | biotools:responsenet, OMICS_01562 | https://bio.tools/responsenet | http://netbio.bgu.ac.il/respnet/ | SCR_003176 | 2026-08-06 09:25:49 | 4 | |||||
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IntEnz- Integrated relational Enzyme database Resource Report Resource Website 10+ mentions |
IntEnz- Integrated relational Enzyme database (RRID:SCR_002992) | IntEnz | database, data or information resource | IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. | enzyme categories, enzyme classification, enzyme nomenclature, enzyme reaction categories, enzyme, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: ENZYME has parent organization: European Bioinformatics Institute has parent organization: SIB Swiss Institute of Bioinformatics |
European Union SLING 226073 | PMID:14681451 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03028, biotools:intenz, r3d100010803 | https://bio.tools/intenz | SCR_002992 | 2026-08-06 09:25:46 | 13 | |||||
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vcflib Resource Report Resource Website 100+ mentions |
vcflib (RRID:SCR_001231) | vcflib | software library, software toolkit, software resource | A C++ library for parsing and manipulating Variant Call Format (VCF) files, and many command-line utilities. The API provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users. | c++, sequence variation, genomic variation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:vcflib, OMICS_02112 | https://bio.tools/vcflib, https://sources.debian.org/src/libvcflib-dev/ | https://sources.debian.org/src/libvcflib-dev/ | SCR_001231 | 2026-08-06 09:25:21 | 119 | ||||||
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CSDeconv Resource Report Resource Website |
CSDeconv (RRID:SCR_000016) | CSDeconv | data analysis software, software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach. | sequence analysis software, transcription factor binding site, chip-seq, blind deconvolution, transcription binding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Rutgers University; New Jersey; USA has parent organization: University of South Australia; Adelaide; Australia |
PMID:20028542 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00436, biotools:csdeconv | https://bio.tools/csdeconv | SCR_000016 | 2026-08-06 09:25:06 | 0 | ||||||
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fastqz Resource Report Resource Website |
fastqz (RRID:SCR_001006) | data management software, source code, software application, software resource | Source code used to compress FASTQ files. FASTQ is DNA sequencing machine output. | compress, source code, fastq output, fastq dna, fastq sequencing, fastq compress, fastq compressor, fastq files, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23533605 | Free, Available for download, Freely available | OMICS_00956, biotools:fastqz | https://bio.tools/fastqz | SCR_001006 | 2026-08-06 09:25:19 | 0 | |||||||
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SeqEM Resource Report Resource Website 1+ mentions |
SeqEM (RRID:SCR_002021) | sequence analysis software, software resource, algorithm resource, data analysis software, data processing software, web application, software application | Online tool for utilizing a genotype calling algorithm for next-generation sequence data. | genotype, algorithm, sequence, rna, dna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Miami Miller School of Medicine; Florida; USA |
PMID:20861027 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00074, biotools:seqem | https://bio.tools/seqem | SCR_002021 | 2026-08-06 09:25:35 | 1 | |||||||
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BeetleBase Resource Report Resource Website 50+ mentions |
BeetleBase (RRID:SCR_001955) | BEETLEBASE | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded. | red flour beetle, tribolium castaneum, sequence data, gene, mutant, genetic marker, expressed sequence tag, genome, blast, model organism, insect, developmental biology, genomics, genetics, entomology, development, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: RefSeq has parent organization: Kansas State University; Kansas; USA |
NCRR P20 RR16475 | PMID:18362917 PMID:17090595 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02599, biotools:beetlebase, r3d100010921 | https://bio.tools/beetlebase, https://doi.org/10.17616/R3G61K | http://bioinformatics.k-state.edu/BeetleBase/, http://www.bioinformatics.ksu.edu/BeetleBase/ | SCR_001955 | 2026-08-06 09:25:34 | 82 | ||||
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SGA Resource Report Resource Website 10+ mentions |
SGA (RRID:SCR_001982) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software package that functions as a de novo genome assembler based on the concept of string graphs. It is designed as a modular set of programs used to assemble large genomes from high coverage short read data. | string, graph assembler, de novo assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
DOI:10.1101/gr.126953.111 | Free, Available for download, Freely available | OMICS_00028, biotools:sga | https://bio.tools/sga, https://sources.debian.org/src/sga/ | SCR_001982 | String Graph Assembler (SGA), String Graph Assembler | 2026-08-06 09:25:34 | 18 | ||||||
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GSNAP Resource Report Resource Website 500+ mentions |
GSNAP (RRID:SCR_005483) | GSNAP | software resource, image analysis software, alignment software, data processing software, software application | Software to align single and paired end reads as short as 14 nt and of arbitrarily long length. Can detect short and long distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or database of known splice sites. Permits SNP-tolerant alignment to reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for study of methylation state. | next-generation sequencing, bio.tools, FASEB list |
is used by: Gsnap2Augustus is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20147302 | OMICS_00665, biotools:gsnap | https://bio.tools/gsnap | SCR_005483 | Genomic Short-read Nucleotide Alignment Program | 2026-08-06 09:26:21 | 784 | ||||||
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EMAGE Gene Expression Database Resource Report Resource Website 10+ mentions |
EMAGE Gene Expression Database (RRID:SCR_005391) | EMAGE | storage service resource, atlas, service resource, data repository, data or information resource, database | A database of in situ gene expression data in the developing mouse embryo and an accompanying suite of tools to search and analyze the data. mRNA in situ hybridization, protein immunohistochemistry and transgenic reporter data is included. The data held is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. The conceptual framework which houses the descriptions of the gene expression patterns in EMAGE is the EMAP Mouse Embryo Anatomy Atlas. This consists of a set of 3D virtual embryos at different stages of development, as well as an accompanying ontology of anatomical terms found at each stage. The raw data images can be conventional 2D photographs (of sections or wholemount specimens) or 3D images of wholemount specimens derived from Optical Projection Tomography (OPT) or confocal microscopy. Users may submit data using a Data submission tool or without. | genetics, 3d model, anatomy, development, mouse morphology, molecular neuroanatomy resource, gene expression, in situ hybridization, immunohistochemistry, embryo, in situ reporter, embryonic mouse, optical projection tomography, confocal microscopy, annotation, pathway, gene association, protein, theiler stage, gene expression, embryology, dna, protein, protein-protein interaction, protein binding, gene, embryology, anatomy, genetics, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: HUDSEN Electronic Atlas of the Developing Human Brain is related to: eMouseAtlas is related to: eMouseAtlas is related to: HUDSEN Human Gene Expression Spatial Database is related to: aGEM is related to: Eurexpress is related to: Gene Expression Database is related to: Gene Ontology is related to: NIDDK Information Network (dkNET) is related to: GUDMAP Ontology |
MRC | PMID:19767607 | Except where noted, Creative Commons Attribution License, The community can contribute to this resource | biotools:emage, nif-0000-00080, r3d100010564 | https://bio.tools/emage, https://doi.org/10.17616/R3860B | SCR_005391 | Emage (e-Mouse Atlas of Gene Expression), e-Mouse Atlas of Gene Expression | 2026-08-06 09:26:25 | 23 | ||||
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ATRHUNTER Resource Report Resource Website 1+ mentions |
ATRHUNTER (RRID:SCR_006480) | ATRHUNTER | software resource, service resource, production service resource, data analysis service, analysis service resource | Software that finds and displays approximate tandem repeats in DNA sequences. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:16201913 | biotools:atrhunter, OMICS_00102 | https://bio.tools/atrhunter | SCR_006480 | 2026-08-06 09:26:35 | 1 | |||||||
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LAST Resource Report Resource Website 100+ mentions |
LAST (RRID:SCR_006119) | LAST | software resource, service resource, production service resource, data analysis service, data processing software, software application, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for aligning sequences, similar to BLAST 2 sequences that colour-codes the alignments by reliability. Another useful feature of LAST is that it can compare huge (vertebrate-genome-sized) datasets. Unfortunately, this only applies to the downloadable version of LAST, not the web service. The web service can just about handle bacterial genomes, but it will take a few minutes and the output will be large. LAST can: * Handle big sequence data, e.g: ** Compare two vertebrate genomes ** Align billions of DNA reads to a genome * Indicate the reliability of each aligned column. * Use sequence quality data properly. * Compare DNA to proteins, with frameshifts. * Compare PSSMs to sequences * Calculate the likelihood of chance similarities between random sequences. LAST cannot (yet): * Do spliced alignment., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence alignment, align, vertebrate, genome, sequence, alignment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: RecountDB has parent organization: National Institute of Advanced Industrial Science and Technology |
National Genome Research Network ; INTEuropean Union Systems Institute ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
PMID:21209072 PMID:20144198 PMID:20110255 DOI:10.1093/nar/gkq010 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151594, biotools:last, OMICS_15813 | https://bio.tools/last, https://sources.debian.org/src/last-align/ | SCR_006119 | 2026-08-06 09:26:31 | 397 | |||||
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GeneCodis Resource Report Resource Website 100+ mentions |
GeneCodis (RRID:SCR_006943) | GeneCodis | software resource, data access protocol, service resource, production service resource, data analysis service, web service, analysis service resource | Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional analysis, gene, annotation, statistical analysis, functional genomics, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: KEGG has parent organization: Spanish National Research Council; Madrid; Spain |
Juan de la Cierva research program ; Spanish Minister of Science and Innovation BIO2010-17527; Government of Madrid P2010/BMD-2305 |
PMID:22573175 PMID:19465387 PMID:17204154 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02221, biotools:genecodis3, nlx_149254 | https://bio.tools/genecodis3 | SCR_006943 | Gene annotations co-ocurrence discovery, GeneCodis - Gene annotations co-ocurrence discovery | 2026-08-06 09:26:43 | 348 | ||||
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ClinVar Resource Report Resource Website 5000+ mentions |
ClinVar (RRID:SCR_006169) | ClinVar | storage service resource, service resource, data repository, data or information resource, database | Archive of aggregated information about sequence variation and its relationship to human health. Provides reports of relationships among human variations and phenotypes along with supporting evidence. Submissions from clinical testing labs, research labs, locus-specific databases, expert panels and professional societies are welcome. Collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about submitter, and other supporting data. Alleles described in submissions are mapped to reference sequences, and reported according to HGVS standard. | sequence variation, variation, phenotype, genetics, genetic variation, clinical, allele, aggregator, geneotype, gene, disease, clinical assertion, bio.tools |
is used by: NIF Data Federation is used by: MARRVEL is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: AutoGVP has parent organization: NCBI |
Free, Freely available | nlx_151671, r3d100013331, biotools:clinvar, OMICS_00262 | https://bio.tools/clinvar, https://doi.org/10.17616/R31NJMS3 | SCR_006169 | 2026-08-06 09:26:31 | 6595 | |||||||
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Candidate Genes to Inherited Diseases Resource Report Resource Website 1+ mentions |
Candidate Genes to Inherited Diseases (RRID:SCR_008190) | G2D | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases. | function, gene, genetic, chromosome, disease, disorder, genome, homology, human, phenotype, protein, region, candidate gene, database, data warehouse, data set, bio.tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Molecular Biology Laboratory has parent organization: EMBL - Bork Group |
PMID:16115313 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21162, biotools:g2d | http://www.bork.embl-heidelberg.de/g2d/, http://www.ogic.ca/projects/g2d_2/, https://bio.tools/g2d | SCR_008190 | G2D - Candidate Genes to Inherited Diseases, Genes2Diseases | 2026-08-06 09:27:06 | 2 | |||||
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FragGeneScan Resource Report Resource Website 100+ mentions |
FragGeneScan (RRID:SCR_011929) | sequence analysis software, software resource, data analysis software, data processing software, software application | A software application for finding fragmented genes in short reads and may be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. | microbiome, sequence analysis, fragment, gene, short read, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: bio.tools is listed by: Debian has parent organization: Indiana University; Indiana; USA |
Acknowledgement requested, Available for download | OMICS_01484, biotools:fraggenescan | http://omics.informatics.indiana.edu/FragGeneScan/, https://bio.tools/fraggenescan | SCR_011929 | 2026-08-06 09:27:51 | 183 | ||||||||
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Vmatch Resource Report Resource Website 10+ mentions |
Vmatch (RRID:SCR_018968) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch, https://sources.debian.org/src/vmatch/ | SCR_018968 | 2026-08-06 09:29:25 | 35 | ||||||||
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LTR_FINDER_parallel Resource Report Resource Website 10+ mentions |
LTR_FINDER_parallel (RRID:SCR_018969) | data analysis software, software application, software resource, data processing software | Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. | Parallelization, rapid identification, retrotransposons identification, repetitive sequences, large genomes, long terminal repeat, retrotrnsposon, parallel operation, bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF IOS 1740874; United States Department of Agriculture National Institute of Food ; Agriculture and AgBioResearch at Michigan State University |
PMID:31857828 | Free, Available for download, Freely available | biotools:LTR_FINDER_parallel | https://bio.tools/LTR_FINDER_parallel | SCR_018969 | 2026-08-06 09:29:30 | 14 | ||||||
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metaXplor Resource Report Resource Website |
metaXplor (RRID:SCR_019025) | web application, data or information resource, software resource | Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures. | Data storage, metagenomics, data filtering, data sharing, data exploration, metagenomic data, viral data, microbial data, data manager, datasets sharing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Restricted | biotools:metaxplor | https://metaxplor.cirad.fr/metaXplor/, https://bio.tools/metaxplor | SCR_019025 | 2026-08-06 09:29:24 | 0 |
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