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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
WSsas - Web Service for the SAS tool
 
Resource Report
Resource Website
WSsas - Web Service for the SAS tool (RRID:SCR_007051) WSsas data access protocol, software resource, web service SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank and provides functional residue annotation based on data from the Catalytic Site Atlas and PDBsum. The web service is aimed to facilitate the use of the SAS tool when having a huge number of queries. Currently, the web service provides annotation for binding sites (to ligand, metal or nucleic acid), catalytic residues and amino acids related to protein-protein interactions. gold standard, bio.tools is listed by: bio.tools
is listed by: Debian
is related to: SAS - Sequence Annotated by Structure
has parent organization: European Bioinformatics Institute
nlx_18182, biotools:wssas https://bio.tools/wssas SCR_007051 Web Service for the SAS tool 2026-09-03 04:48:54 0
CD-HIT
 
Resource Report
Resource Website
1000+ mentions
CD-HIT (RRID:SCR_007105) CD-HIT data processing software, software application, software resource, source code THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for clustering biological sequences with many applications in various fields such as making non-redundant databases, finding duplicates, identifying protein families, filtering sequence errors and improving sequence assembly etc. It is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU and over a dozen scripts. * CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. * CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. * CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads. * CD-HIT-OTU cluster rRNA tags into OTUs The usage of other programs and scripts can be found in CD-HIT user''s guide. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik''s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. cluster, protein, sequence, classification, domain, analysis, nucleotide sequence, dna, protein sequence, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
has parent organization: University of California at San Diego; California; USA
has parent organization: Google Code
is parent organization of: CD-HIT-OTU
NCRR 1R01RR025030 PMID:20053844
PMID:16731699
DOI:10.1093/bioinformatics/btl158
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_05157, biotools:cd-hit, nif-0000-30240 http://cd-hit.org, https://code.google.com/p/cdhit/, https://bio.tools/cd-hit, https://sources.debian.org/src/cd-hit/ http://bioinformatics.ljcrf.edu/cd-hi/
SCR_007105 CD-HIT Program 2026-09-03 04:49:01 3223
Expression Database in 4D
 
Resource Report
Resource Website
1+ mentions
Expression Database in 4D (RRID:SCR_007066) 4DXpress data or information resource, data repository, database, service resource, storage service resource This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The name 4DXpress stands for expression database in 4D. The 4D (four dimensions) of 4DXpress can be interpreted either as: 3 spatial dimensions plus time, or as 1. species 2. gene 3. developmental stage 4. anatomical structure. The major focus of this database lies in cross species comparison. The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments. Data was integrated from several species specific expression pattern databases, such as ZFIN, BDGP, GXD, MEPD as well as directly submitted by researchers of the participating groups at EMBL. The 4DXpress database is a project within the Centre for Computational Biology at EMBL. It is developed by Yannick Haudry, Thorsten Henrich and Ivica Letunic and coordinated by Thorsten Henrich. Hugo Berube is developing the 4D ArrayExpress Data Warehouse at EBI for integrating in situ data with microarray data. genes, anatomical structures, developmental stage, microarray data, species, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: European Molecular Biology Laboratory
European Molecular Biology Laboratory; Heidelberg; Germany PMID:17916571 nif-0000-02524, biotools:4dxpress https://bio.tools/4dxpress SCR_007066 4DXpress Database 2026-09-03 04:49:06 1
Chromosome 7 Annotation Project
 
Resource Report
Resource Website
10+ mentions
Chromosome 7 Annotation Project (RRID:SCR_007134) Chromosome 7 Annotation Project data or information resource, data repository, database, service resource, storage service resource Database containing the DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented; the most up to date collation of sequence, gene, and other annotations from all databases (eg. Celera published, NCBI, Ensembl, RIKEN, UCSC) as well as unpublished data. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. The objective of this project is to generate a comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications. There are over 360 disease-associated genes or loci on chromosome 7. A major challenge ahead will be to represent chromosome alterations, variants, and polymorphisms and their related phenotypes (or lack thereof), in an accessible way. In addition to being a primary data source, this site serves as a weighing station for testing community ideas and information to produce highly curated data to be submitted to other databases such as NCBI, Ensembl, and UCSC. Therefore, any useful data submitted will be curated and shown in this database. All Chromosome 7 genomic clones (cosmids, BACs, YACs) listed in GBrowser and in other data tables are freely distributed. duplication, gene expression, family, fish, gene, gene annotation, genome, breakpoint, chromosome, chromosome 7, clinical, deletion, disease, dna sequence, human, insertion, inversion, polymorphism, rearrangement, segmental duplication, snp, translocation, annotation, data analysis service, blat, cosmid, bac, yac, biomaterial supply resource, malignant, non malignant, bio.tools is listed by: One Mind Biospecimen Bank Listing
is listed by: Debian
is listed by: bio.tools
PMID:12690205 Free, (Genomic clones) nif-0000-03550, biotools:chr7, r3d100012136 https://bio.tools/chr7, https://doi.org/10.17616/R3VP9V SCR_007134 The Chromosome 7 Annotation Project, Chromosome 7 Annotation Project 2026-09-03 04:49:08 13
Biological General Repository for Interaction Datasets (BioGRID)
 
Resource Report
Resource Website
1000+ mentions
Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) BioGRID data or information resource, database Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts. budding yeast, fission yeast, protein, gene, protein interaction, genetic interaction, model organism, interaction, dataset, gene annotation, phenotype, orthologous interaction, yeast, cellular interaction network, physical interaction, protein-peptide, protein-rna, protein-protein interaction, genetics, publication, raw protein, genetic interaction, web service, pathway, network, biology, gene mapping, statistics, bio.tools, FASEB list is used by: NIF Data Federation
is recommended by: National Library of Medicine
is recommended by: NIDDK Information Network (dkNET)
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: DataCite
is listed by: NIH Data Sharing Repositories
is listed by: bio.tools
is listed by: Debian
is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions
is related to: Pathway Commons
is related to: Cytoscape
is related to: Interaction Reference Index
is related to: ConsensusPathDB
is related to: FlyMine
is related to: IMEx - The International Molecular Exchange Consortium
is related to: Integrated Molecular Interaction Database
is related to: PSICQUIC Registry
is related to: PSI-MI
is related to: NIH Data Sharing Repositories
is related to: Agile Protein Interactomes DataServer
is related to: Integrated Manually Extracted Annotation
has parent organization: Princeton University; New Jersey; USA
has parent organization: University of Edinburgh; Scotland; United Kingdom
has parent organization: University of Montreal; Quebec; Canada
works with: IMEx - The International Molecular Exchange Consortium
BBSRC ;
Canadian Institutes of Health Research ;
NCRR R01 RR024031;
NHGRI HG02223;
NIH Office of the Director R24 OD011194
PMID:23203989
PMID:21071413
PMID:16381927
PMID:12620108
Free, Freely available nif-0000-00432, r3d100010350, OMICS_01901, biotools:the_grid https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources, https://bio.tools/the_grid, https://doi.org/10.17616/R34C7G SCR_007393 , BioGRID, Biological General Repository for Interaction Datasets 2026-09-03 04:49:34 2824
FlexProt: flexible protein alignment
 
Resource Report
Resource Website
1+ mentions
FlexProt: flexible protein alignment (RRID:SCR_007306) software resource FlexProt detects the optimal flexible structural alignment of a pair of protein structures. The first structure is assumed to be rigid, while in the second structure potential flexible regions are automatically detected. bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Tel Aviv University; Ramat Aviv; Israel
nif-0000-00159, biotools:flexprot https://bio.tools/flexprot SCR_007306 FlexPROT 2026-09-03 04:49:18 1
Electronic Cell Project
 
Resource Report
Resource Website
10+ mentions
Electronic Cell Project (RRID:SCR_007381) modeling software, simulation software, software application, software resource Software platform, general technologies and theoretical supports for computational biology with the grand aim to make precise whole cell simulation at the molecular level possible.Technologies include formalisms and techniques, including technologies to predict, obtain or estimate parameters such as reaction rates and concentrations of molecules in the cell. The E-Cell System is a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale system like the cell. The E-Cell Project is open to anyone who shares the view with u that development of cell simulation technology, and, even if such ultimate goal might not be within ten years of reach yet, solving various conceptual, computational and experimental problems that will continue to arise in the course of pursuing it, may have a multitude of eminent scientific, medical and engineering impacts on our society. gene, protein, ontology, binary executable; software development tool, cell is listed by: Debian nif-0000-00378 https://sources.debian.org/src/ecell/ SCR_007381 E-Cell 2026-09-03 04:49:17 15
Taipan
 
Resource Report
Resource Website
1+ mentions
Taipan (RRID:SCR_007330) Taipan software resource A fast hybrid short-read assembly tool. c, unix/linux, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: SourceForge
PMID:19535537 GNU General Public License, v2 OMICS_00035, biotools:taipan https://bio.tools/taipan SCR_007330 2026-09-03 04:49:04 2
GenoTan
 
Resource Report
Resource Website
1+ mentions
GenoTan (RRID:SCR_007935) GenoTan software resource A free software tool to identify length variation of microsatellites from short sequence reads. bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: SourceForge
PMID:24135263 GNU General Public License, v3 biotools:genotan https://bio.tools/genotan SCR_007935 GenoTan - Genotyping of microsatellite loci 2026-09-03 04:49:28 1
VISTA Enhancer Browser
 
Resource Report
Resource Website
100+ mentions
VISTA Enhancer Browser (RRID:SCR_007973) VISTA Enhancer Browser data or information resource, data repository, database, service resource, storage service resource Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth. human, noncoding fragment, mutant mouse strain, molecular neuroanatomy resource, image, telencephalon, development, genome, enhancer, dna fragment, embryo, embryonic mouse, brain, neural tube, eye, ear, heart, tail, limb, nose, cranial nerve, trigeminal, dorsal root ganglia, face, branchial arch, gene expression, annotation, vector, transgenic embryo, lacz reporter vector, lacz, biomaterial supply resource, in vivo, image collection, transcriptional enhancer, chip-seq, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
is related to: NIF Data Federation
is related to: One Mind Biospecimen Bank Listing
is related to: OMICtools
has parent organization: Lawrence Berkeley National Laboratory
American Heart Association ;
DOE contract DE-AC02-05CH11231;
DOE DE020060;
NHGRI HG003988;
NHLBI HL066681;
NIDCR ;
NINDS NS062859
PMID:17130149 Free, Freely available nif-0000-03637, OMICS_01568, biotools:vista_enhancer_browser https://bio.tools/vista_enhancer_browser SCR_007973 2026-09-03 04:49:31 249
T1DBase
 
Resource Report
Resource Website
100+ mentions
T1DBase (RRID:SCR_007959) data or information resource, data repository, database, resource, service resource, storage service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://immunobase.org). Documented on March 2020, ImmunoBase ownership has been transferred to Open Targets (https://www.opentargets.org). Results for all studies can be explored using Open Targets Genetics (https://genetics.opentargets.org). Database focused on genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data. genetics, beta cell, gene, variant, region, genomics, gene expression, genome-wide association study, data analysis service, bio.tools is used by: NIF Data Federation
is used by: NIDDK Information Network (dkNET)
is listed by: NIDDK Information Network (dkNET)
is listed by: Debian
is listed by: bio.tools
is related to: dkCOIN
has parent organization: University of Cambridge; Cambridge; United Kingdom
Type 1 diabetes. Diabetes Wellcome Trust ;
NIDDK ;
Juvenile Diabetes Research Foundation
PMID:20937630 THIS RESOURCE IS NO LONGER IN SERVICE. nif-0000-03531, biotools:t1dbase https://bio.tools/t1dbase SCR_007959 T1DBase - Type 1 Diabetes Database 2026-09-03 04:49:18 147
HilbertVis
 
Resource Report
Resource Website
1+ mentions
HilbertVis (RRID:SCR_007862) HilbertVis software resource Software tool that allows to display very long data vectors in a space-efficient manner, allowing the user to visually judge the large scale structure and distribution of features simultaneously with the rough shape and intensity of individual features. bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: European Bioinformatics Institute
DOI:10.1093/bioinformatics/btp152 OMICS_00627, biotools:hilbertvis https://bio.tools/hilbertvis, https://sources.debian.org/src/r-bioc-hilbertvis/ SCR_007862 2026-09-03 04:49:16 4
BRIG
 
Resource Report
Resource Website
500+ mentions
BRIG (RRID:SCR_007802) BRIG software resource A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: SourceForge
DOI:10.1186/1471-2164-12-402 OMICS_00929, biotools:brig https://bio.tools/brig, https://sources.debian.org/src/brig/ SCR_007802 BLAST Ring Image Generator 2026-09-03 04:49:27 561
dbEST
 
Resource Report
Resource Website
100+ mentions
dbEST (RRID:SCR_008132) data or information resource, data repository, database, service resource, storage service resource Database as a division of GenBank that contains sequence data and other information on single-pass cDNA sequences, or Expressed Sequence Tags, from a number of organisms. data, sequence, single, pass, cDNA, express, tag, bio.tools, gold standard is listed by: Debian
is listed by: bio.tools
has parent organization: NCBI
PMID:8401577 biotools:dbest, nif-0000-20937, r3d100010648 http://www.ncbi.nlm.nih.gov/dbEST/, https://bio.tools/dbest, https://doi.org/10.17616/R3FG8P SCR_008132 database Expressed Sequence Tag (EST), database Expressed Sequence Tag 2026-09-03 04:49:50 186
lobSTR
 
Resource Report
Resource Website
10+ mentions
lobSTR (RRID:SCR_008030) lobSTR software resource A software tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data., 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
has parent organization: Massachusetts Institute of Technology; Massachusetts; USA;
PMID:22522390 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00109, biotools:lobstr https://bio.tools/lobstr SCR_008030 lobSTR - Profiling STRs in personal genomes 2026-09-03 04:49:33 47
ActiveDriver
 
Resource Report
Resource Website
10+ mentions
ActiveDriver (RRID:SCR_008104) ActiveDriver data analysis software, data processing software, sequence analysis software, software application, software resource A statistical method for interpreting variations in protein sequence (e.g. coding SNPs in the population, SNVs in cancer genomes) in the context of protein post-translational signaling modifications. Protein sequence variation, variation interpretation, protein sequence, protein post-translational signaling modifications, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
Free, Available for download, Freely available biotools:ActiveDriver, OMICS_00140 http://reimandlab.org/software/activedriver/, https://cran.r-project.org/web/packages/ActiveDriver/ActiveDriver.pdf, https://bio.tools/ActiveDriver SCR_008104 2026-09-03 04:49:36 27
QIIME
 
Resource Report
Resource Website
10000+ mentions
QIIME (RRID:SCR_008249) data analysis software, data processing software, software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics. microbiome, microbial community, sequence data, data analysis software, bio.tools is used by: SortMeRNA
is used by: Nephele
is listed by: OMICtools
is listed by: Human Microbiome Project
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
has parent organization: University of Colorado Boulder; Colorado; USA
DOI:10.1038/nmeth.f.303 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01118, SCR_011948, OMICS_01521, biotools:qiime https://bio.tools/qiime SCR_008249 Quantitative Insights Into Microbial Ecology 2026-09-03 04:49:26 11177
IsaCGH
 
Resource Report
Resource Website
IsaCGH (RRID:SCR_008375) IsaCGH software resource Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations. microarray, array cgh, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
OMICS_00727, biotools:isacgh https://bio.tools/isacgh SCR_008375 2026-09-03 04:49:58 0
G protein receptor interaction feature finding instrument
 
Resource Report
Resource Website
10+ mentions
G protein receptor interaction feature finding instrument (RRID:SCR_008343) analysis service resource, production service resource, resource, service resource Griffin (G-protein-receptor interacting feature finding instrument) is a high-throughput system to predict GPCR - G-protein coupling selectively with the input of GPCR sequence and ligand molecular weight. This system consists of two parts: 1) HMM section using family specific multiple alignment of GPCRs, 2) SVM section using physico-chemical feature vectors in GPCR sequence. G-protein coupled receptors (GPCR), which is composed of seven transmembrane helices, play a role as interface of signal transduction. The external stimulation for GPCR, induce the coupling with G-protein (Gi/o, Gq/11, Gs, G12/13) followed by different kinds of signal transduction to inner cell. About half of distributed drugs are intending to control this GPCR - G-protein binding system, and therefore this system is important research target for the development of effective drug. For this purpose, it is necessary to monitor, effectively and comprehensively, of the activation of G-protein by identifying ligand combined with GPCR. Since, at present, it is difficult to construct such biochemical experiment system, if the answers for experimental results can be prepared beforehand by using bioinformatics techniques, large progress is brought to G-protein related drug design. Previous works for predicting GPCR-G protein coupling selectivity are using sequence pattern search, statistical models, and HMM representations showed high sensitivity of predictions. However, there are still no works that can predict with both high sensitivity and specificity. In this work we extracted comprehensively the physico-chemical parameters of each part of ligand, GPCR and G-protein, and choose the parameters which have strong correlation with the coupling selectivity of G-protein. These parameters were put as a feature vector, used for GPCR classification based on SVM. drug, alignment, biochemical, bioinformatic, coupling, gpcr, g-protein, helix, instrument, interface, ligand, molecular, pattern, physico-chemical, receptor interacting, sequence, signal transduction, stimulation, svm, system, technique, transmembrane, weight, instrument, equipment, hardware, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Computational Biology Research Center Core Facility
National Institute of Advanced Industrial Science and Technology nif-0000-25210, biotools:griffin https://bio.tools/griffin SCR_008343 Griffin 2026-09-03 04:49:34 21
SeWeR - SEquence analysis using WEb Resources
 
Resource Report
Resource Website
SeWeR - SEquence analysis using WEb Resources (RRID:SCR_004167) data or information resource, portal, service resource, software resource, topical portal Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. It doesn''t require any server to host itself. The goal of SeWeR is to turn your web-browser into a powerful sequence-analysis tool. It is written entirely in JavaScript1.2. SeWeR can be downloaded and mirrored freely. The whole package is just around 300K. You can even run it from a floppy. SeWeR is not compatible with Netscape 6. SeWeR now generates graphics. Savvy is a plasmid drawing software that generates plasmid map in the revolutionary Scalable Vector Graphics format from W3C. nucleic acid, protein, pcr, alignment, sequence, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: Centre for Cellular and Molecular Biology; Hyderabad; India
PMID:11395442 biotools:sewer, nlx_18981 https://bio.tools/sewer SCR_004167 SEquence analysis using WEb Resources, SeWeR 2026-09-03 04:46:54 0

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