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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
ANNOVAR
 
Resource Report
Resource Website
5000+ mentions
ANNOVAR (RRID:SCR_012821) ANNOVAR software application, software resource An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software) genomic analysis, imaging genomics, next generation sequencing, snp, gene, bio.tools is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: wANNOVAR
has parent organization: OpenBioinformatics.org
PMID:20601685 Free nlx_154225, biotools:annovar, OMICS_00165 https://bio.tools/annovar, https://bio.tools/annovar SCR_012821 functional ANNOtation of genetic VARiants, ANNOVAR: Functional annotation of genetic variants 2026-09-19 12:58:08 6463
SASQUANT
 
Resource Report
Resource Website
1+ mentions
SASQUANT (RRID:SCR_013122) software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program to estimate genetic effects and heritabilities of quantitative traits in breeding populations consisting of six related generations (entry from Genetic Analysis Software) gene, genetic, genomic, sas, bio.tools is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
THIS RESOURCE IS NO LONGER IN SERVICE nlx_154610, biotools:sasquant https://bio.tools/sasquant SCR_013122 2026-09-19 12:58:09 4
QMSIM
 
Resource Report
Resource Website
50+ mentions
QMSIM (RRID:SCR_013123) software application, software resource Software application designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data. (entry from Genetic Analysis Software) gene, genetic, genomic, c++, ms-windows, linux, bio.tools is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
nlx_154560, biotools:qmsim https://bio.tools/qmsim SCR_013123 Qtl and Marker SIMulator 2026-09-19 12:58:09 63
rSNP Guide
 
Resource Report
Resource Website
1+ mentions
rSNP Guide (RRID:SCR_000087) data or information resource, database A system of databases which stores information on the influence of mutations in regulatory gene regions . This tool helps recognize protein binding sites that are being altered by mutation. It has four cross-linked sub databases that focus on specific aspects including: (1) the effect of single nucleotide mutations in regulatory gene regions and their interaction with nuclear proteins; (2) references to original publications on the subject; (3) the experimental details of these publications; and (4) the protocols of these experiments. This resource is aimed at providing information to further research on the influence of specific sequence alterations on disease susceptibility, drug resistance and healthcare. database, single nucleotide mutations, RNA, DNA, nuclear proteins, protein binding sites, drug resistance, disease susceptibility, health care, regulatory gene regions, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Siberian Branch of the Russian Academy of Sciences; Novosibirsk; Russia
Open Source nif-0000-03428, biotools:rsnp_guide https://bio.tools/rsnp_guide SCR_000087 rSNP Guide 2026-09-19 12:56:25 1
Interolog/Regulog Database
 
Resource Report
Resource Website
1+ mentions
Interolog/Regulog Database (RRID:SCR_000755) data or information resource, database Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. interacting, interolog, protein, regulog, sequence, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Yale University; Connecticut; USA
PMID:15173116 nif-0000-20863, biotools:interolog https://bio.tools/interolog SCR_000755 Interolog 2026-09-19 12:56:28 2
ProGlycProt
 
Resource Report
Resource Website
1+ mentions
ProGlycProt (RRID:SCR_000622) ProGlycProt data or information resource, database Manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. The database is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoproteins, defined as entries with at least one experimentally known glycosylated residue (glycosite). Whereas, ProUGP is the supplementary section, presenting uncharacterized prokaryotic glycoproteins, defined as entries with experimentally identified glycosylation but unidentified glycosites. The ProGlycProt has been developed with to aid and advance the emerging scientific interests in understanding the mechanisms, implications, and novelties of protein glycosylation in prokaryotes that include many pathogenic as well as economically important bacterial species. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology. A general data update policy is once in three months. Existing entries are updated in real-time. glycoprotein, glycosite, glycosylation, coding gene, protein, glycosylation type, attached glycan, oligosaccharyl transferase, glycosyl transferase, glycobiology, glycosylating enzyme, glycosylation linked gene, crystal structure, homology, homology model, blast, predict, bacteria, archaea, image collection, structure, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Institute of Microbial Technology; Chandigarh; India
Institute of Microbial Technology; Chandigarh; India OLP0063;
Council of Scientific and Industrial Research; New Delhi; India SIP10AA
PMID:22039152 nlx_151583, biotools:proglycprot https://bio.tools/proglycprot SCR_000622 Prokaryotic Glycoproteins, ProGlycProt - A Repository of Experimentally Characterized GlycoProteins of Prokaryotes 2026-09-19 12:56:27 1
dbSTS
 
Resource Report
Resource Website
1+ mentions
dbSTS (RRID:SCR_000400) dbSTS data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences. genomic, mapping, sequence, gold standard, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: NCBI
NIH PMID:2781285 THIS RESOURCE IS NO LONGER IN SERVICE biotools:dbsts, nif-0000-20939, r3d100010649 https://bio.tools/dbsts, https://doi.org/10.17616/R39P5C SCR_000400 NCBI dbSTS: database of Sequence Tagged Sites, Sequence Tagged Sites Database, NCBI dbSTS, dbSTS: database of Sequence Tagged Sites, Database of Sequence Tagged Sites 2026-09-19 12:56:26 3
AnimalTFDB
 
Resource Report
Resource Website
100+ mentions
AnimalTFDB (RRID:SCR_001624) AnimalTFDB data or information resource, database A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. transcription factor, dna-binding domain, transcription co-factor, chromatin remodeling factor, gene structure, functional domain, go annotation, protein interaction, ortholog, paralog, 3d structure, pathway, protein-protein interaction, binding site, target, data set, image collection, 3d spatial image, bio.tools, FASEB list is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
is related to: Ensembl
has parent organization: Huazhong University of Science and Technology; Wuhan; China
Huazhong University of Science and Technology; Wuhan; China ;
Fundamental Research Funds for the Central Universities 2010MS045;
National Natural Science Foundation of China 31171271
PMID:22080564 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01856, nlx_153892, biotools:animal_tfdb https://bio.tools/animal_tfdb SCR_001624 Animal Transcription Factor Database 2026-09-19 12:56:31 292
Human Gene Mutation Database
 
Resource Report
Resource Website
1000+ mentions
Human Gene Mutation Database (RRID:SCR_001621) HGMD data or information resource, database Curated database of known (published) gene lesions responsible for human inherited disease. gene, disease, gene lesion, mutation, deletion, insertion, duplication, rearrangement, nuclear gene, functional polymorphism, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: BIOBASE Corporation
has parent organization: Cardiff University; Wales; United Kingdom
Inherited disease PMID:22948725
PMID:20368137
PMID:20038494
PMID:19348700
PMID:18428754
PMID:18245393
PMID:12754702
PMID:10612821
PMID:9399854
PMID:9066272
PMID:8882888
Free, Freely available nlx_153887, SCR_001888, biotools:hgmd, nif-0000-10459, OMICS_00281 http://www.hgmd.cf.ac.uk/ac/index.php, https://bio.tools/hgmd, SCR_001621 The Human Gene Mutation Database, The Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff 2026-09-19 12:56:31 2682
COSMIC - Catalogue Of Somatic Mutations In Cancer
 
Resource Report
Resource Website
1000+ mentions
COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) COSMIC data or information resource, database Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats.
Some key features of COSMIC are:
* Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types.
* Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines.
cancer, mutation, somatic mutation, tumor, cancer genome, genome, gene, dna, tissue, histology, bio.tools, FASEB list is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Cancer Wellcome Trust 077012/Z/05/Z PMID:20952405 Free nif-0000-02690, biotools:cosmic, OMICS_00082 http://www.sanger.ac.uk/perl/CGP/cosmic, https://bio.tools/cosmic SCR_002260 Catalogue Of Somatic Mutations In Cancer 2026-09-19 12:56:34 4809
HOMOZYGOSITYMAPPER
 
Resource Report
Resource Website
100+ mentions
HOMOZYGOSITYMAPPER (RRID:SCR_001714) HomozygosityMapper analysis service resource, data analysis service, production service resource, service resource A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software) gene, genetic, genomic, perl, genotype, homozygosity score, homozygosity, bio.tools, FASEB list is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: bio.tools
is listed by: Debian
has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany
PMID:19465395 Free, Freely Available nlx_154069, biotools:homozygositymapper, OMICS_00123 https://bio.tools/homozygositymapper SCR_001714 2026-09-19 12:56:31 125
WebGeSTer DB
 
Resource Report
Resource Website
1+ mentions
WebGeSTer DB (RRID:SCR_002165) WebGeSTer DB data or information resource, database Database of intrinsic terminators of transcription that is comprized of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. Information about structural parameters of individual terminators such as sequence, length of stem and loop, mismatches and gaps, U-trail, genomic coordinates and gene name and accession number is available in both tabular form and as a composite figure. Summary statistics for terminator profiles of whole genome can be also obtained. Raw data files for individual genomes can be downloaded (.zip files) for detailed investigations. Data is organized into different tiers such that users can fine-tune their search by entering name of the species, or taxon ID or genomes with a certain number of terminators. To visualize the occurrence of the terminators, an interactive map, with the resolution to single gene level, has been developed. genome, terminator, transcription, plasmid, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
PMID:20972211 THIS RESOURCE IS NO LONGER IN SERVICE biotools:webgester_db, OMICS_01862 https://bio.tools/webgester_db SCR_002165 WebGesTer Database, Web Genome Scannner for Terminators Database, WebGeSTer DB - A Transcription Terminator Database 2026-09-19 12:56:34 5
PubGene
 
Resource Report
Resource Website
10+ mentions
PubGene (RRID:SCR_002119) data or information resource, database It helps users retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a gene-centric database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a literature network organizing information in a form that is easy to navigate. gene, information, protein, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
is parent organization of: Coremine Medical
Free, Freely Available biotools:pubgene, nif-0000-20908 https://bio.tools/pubgene SCR_002119 PubGene 2026-09-19 12:56:33 39
EchoBASE
 
Resource Report
Resource Website
1+ mentions
EchoBASE (RRID:SCR_002430) EchoBASE data or information resource, database A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium. gene, bio.tools is listed by: bio.tools
is listed by: Debian
GlaxoSmithKline ;
BBSRC
PMID:15608209 nif-0000-02781, biotools:echobase, r3d100011646 https://bio.tools/echobase, https://doi.org/10.17616/R38W6H SCR_002430 EchoBASE: an integrated post-genomic database for Escherichia coli 2026-09-19 12:56:36 6
Autophagy Database
 
Resource Report
Resource Website
10+ mentions
Autophagy Database (RRID:SCR_002671) Autophagy DB, AutophagyDB data or information resource, database Database that provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in eukaryotes. autophagy, protein, homolog, ortholog, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Tokyo; Tokyo; Japan
Japanese Ministry of Education Culture Sports Science and Technology MEXT PMID:20972215 Free, Available for download, Freely available OMICS_03306, biotools:the_autophagy_database, r3d100012565 https://bio.tools/the_autophagy_database, https://doi.org/10.17616/R3J786 SCR_002671 2026-09-19 12:56:36 22
DOMINE: Database of Protein Interactions
 
Resource Report
Resource Website
1+ mentions
DOMINE: Database of Protein Interactions (RRID:SCR_002399) DOMINE data or information resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Database of known and predicted protein domain (domain-domain) interactions containing interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions. DOMINE contains a total of 26,219 domain-domain interactions (among 5,410 domains) out of which 6,634 are inferred from PDB entries, and 21,620 are predicted by at least one computational approach. Of the 21,620 computational predictions, 2,989 interactions are high-confidence predictions (HCPs), 2,537 interactions are medium-confidence predictions (MCPs), and the remaining 16,094 are low-confidence predictions (LCPs). (May 2014) domain-domain interaction, prediction, protein domain, interaction, protein domain interaction, protein, domain, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
is related to: Pfam
has parent organization: University of Texas at Dallas; Texas; USA
PMID:21113022
PMID:17913741
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01906, nif-0000-02758, biotools:domine https://bio.tools/domine SCR_002399 Database of Protein Domain Interactions 2026-09-19 12:56:36 2
VIPERdb
 
Resource Report
Resource Website
50+ mentions
VIPERdb (RRID:SCR_002853) data or information resource, database Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. exploration, analysis, capsid, computational, convention, database, icosahedral, structural, structure, system, virus, visual, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
has parent organization: Scripps Research Institute
PMID:33313778
PMID:30265627
Free, Freely available nif-0000-25311, r3d100012362, nif-0000-03630, biotools:viperdb, SCR_007970 https://bio.tools/viperdb, https://doi.org/10.17616/R3HT0Q SCR_002853 Virus Particle ExploreR 2026-09-19 12:56:37 59
Human Gene Connectome Server
 
Resource Report
Resource Website
1+ mentions
Human Gene Connectome Server (RRID:SCR_002627) HGCS analysis service resource, data analysis service, production service resource, service resource An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways. gene, disease, phenotype, genome, connectome, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Human Gene Connectome
PMID:23509278 Free nlx_156049, biotools:hgcs https://bio.tools/hgcs SCR_002627 2026-09-19 12:56:36 8
Nucleic Acid Database
 
Resource Report
Resource Website
10+ mentions
Nucleic Acid Database (RRID:SCR_003255) NDB data or information resource, database A database of three-dimensional structural information about nucleic acids and their complexes. In addition to primary data, it contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. NDB maintains the macromolecular Crystallographic Information File (mmCIF). nucleic acid, dna, nucleopeptide, nucleoprotein, nucleotide, rna, transfection, sequence, structure, function, bio.tools, FASEB list is listed by: re3data.org
is listed by: bio.tools
is listed by: Debian
is related to: MINAS - Metal Ions in Nucleic AcidS
is related to: Biological Magnetic Resonance Data Bank (BMRB)
is related to: Jenalib: Jena Library of Biological Macromolecules
has parent organization: Rutgers University; New Jersey; USA
NSF ;
DOE ;
NIH
PMID:24185695
PMID:1384741
Free, Available for download, Freely available nif-0000-03184, biotools:ndb, r3d100010415 https://bio.tools/ndb, https://doi.org/10.17616/R3531R SCR_003255 2026-09-19 12:56:39 37
RefSeq
 
Resource Report
Resource Website
10000+ mentions
RefSeq (RRID:SCR_003496) data or information resource, database Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases. reference sequence, transcript, protein, dna, rna, plasmid, organelle, virus, genome, nucleic acid, ortholog, paralog, haplotype, nucleotide sequence, gene expression, blast, gold standard, bio.tools is listed by: OMICtools
is listed by: re3data.org
is listed by: bio.tools
is listed by: Debian
is related to: BeetleBase
is related to: EcoGene
is related to: INSDC
is related to: HFV Database
is related to: RefSeqGene
is related to: NCBI Protein Database
is related to: RefSeqGene
is related to: UniParc at the EBI
is related to: NCBI Nucleotide
is related to: UniParc
is related to: ProRepeat
is related to: NCBI Virus
is related to: Codon and Codon-Pair Usage Tables
is related to: RefSeq non-redundant proteins
has parent organization: NCBI
PMID:24316578
PMID:24259432
PMID:22121212
PMID:18927115
PMID:17130148
PMID:15608248
Free, Available for download, Freely available SCR_016579, nif-0000-03397, OMICS_01659, biotools:refseq, r3d100011306 ftp://ftp.ncbi.nlm.nih.gov/refseq, https://bio.tools/refseq, https://doi.org/10.17616/R3HP70 SCR_003496 RefSeq, , Reference Sequence Database, Reference Sequence, Reference Sequences, NCBI 2026-09-19 12:56:40 19506

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