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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | SciCrunch Registry | FlexPROT | 2026-10-24 12:45:55 | 1 | ||||||||
|
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 | SciCrunch Registry | 2026-10-24 12:45:56 | 2 | ||||||
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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 | SciCrunch Registry | GenoTan - Genotyping of microsatellite loci | 2026-10-24 12:46:00 | 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 | SciCrunch Registry | 2026-10-24 12:46:01 | 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 | SciCrunch Registry | T1DBase - Type 1 Diabetes Database | 2026-10-24 12:46:00 | 147 | ||||
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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 | SciCrunch Registry | 2026-10-24 12:46:01 | 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 | SciCrunch Registry | BLAST Ring Image Generator | 2026-10-24 12:46:00 | 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 | SciCrunch Registry | database Expressed Sequence Tag (EST), database Expressed Sequence Tag | 2026-10-24 12:46:04 | 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 | SciCrunch Registry | lobSTR - Profiling STRs in personal genomes | 2026-10-24 12:46:02 | 47 | |||||
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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 | SciCrunch Registry | 2026-10-24 12:46:03 | 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 | SciCrunch Registry | Quantitative Insights Into Microbial Ecology | 2026-10-24 12:46:03 | 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 | SciCrunch Registry | 2026-10-24 12:46:07 | 0 | ||||||||
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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 | SciCrunch Registry | Griffin | 2026-10-24 12:46:04 | 21 | |||||||
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CAT Resource Report Resource Website 10+ mentions |
CAT (RRID:SCR_008421) | CAT | software resource | A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01676, biotools:CAt | https://bio.tools/CAT | SCR_008421 | SciCrunch Registry | 2026-10-24 12:46:05 | 13 | |||||||
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Geneious Resource Report Resource Website 10000+ mentions |
Geneious (RRID:SCR_010519) | data analysis software, data management software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools. | Sequence alignment software, data management software, analysis software, Geneious Biologics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is parent organization of: Geneious Microsatellite Plugin |
PMID:22543367 | Restricted | OMICS_00016, biotools:geneious | http://nebc.nerc.ac.uk/news/geneiousonbl, https://bio.tools/geneious | SCR_010519 | SciCrunch Registry | Geneious Prime, Geneious 11.0, Geneious 11.1.2, Geneious 8.1, Geneious Basic | 2026-10-24 12:46:21 | 13589 | ||||||
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HMCan Resource Report Resource Website 10+ mentions |
HMCan (RRID:SCR_010858) | HMCan | software resource | A Hidden Markov Model based software tool that is developed to detect histone modification in cancer ChIP-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:24021381 | biotools:hmcan, OMICS_00443 | https://bio.tools/hmcan | SCR_010858 | SciCrunch Registry | Histone Modification in Cancer | 2026-10-24 12:46:24 | 14 | ||||||
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CNVer Resource Report Resource Website 1+ mentions |
CNVer (RRID:SCR_010820) | CNVer | software resource | A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:cnver, OMICS_00341 | https://bio.tools/cnver | SCR_010820 | SciCrunch Registry | 2026-10-24 12:46:24 | 8 | ||||||||
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Relate Resource Report Resource Website 10+ mentions |
Relate (RRID:SCR_010794) | Relate | software resource | Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:19025785 | biotools:relateadmix, OMICS_00207 | https://bio.tools/relateadmix | SCR_010794 | SciCrunch Registry | 2026-10-24 12:46:23 | 47 | |||||||
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MoDIL Resource Report Resource Website 1+ mentions |
MoDIL (RRID:SCR_010764) | MoDIL | software resource | Software for a novel method for finding medium sized indels from high throughput sequencing datasets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Toronto; Ontario; Canada |
OMICS_00066, biotools:modil | https://bio.tools/modil | SCR_010764 | SciCrunch Registry | MoDIL: Detecting INDEL Variation with Clone-end Sequencing | 2026-10-24 12:46:23 | 4 | |||||||
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MISA Resource Report Resource Website 1000+ mentions |
MISA (RRID:SCR_010765) | MISA | software resource | Software tool that allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00110, biotools:misa | https://bio.tools/misa | SCR_010765 | SciCrunch Registry | MISA - MIcroSAtellite identification tool | 2026-10-24 12:46:23 | 1053 |
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