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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | ||||||
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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 | |||||
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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 | |||||
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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 | ||||||
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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 | ||||||
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SNPAAMapper Resource Report Resource Website |
SNPAAMapper (RRID:SCR_002012) | SNPAAMapper | data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5?UTR, etc). Major features: * The pipeline accepts the VCF (Variant Call Format) input file in tab-delimited format and processes the vcf input file containing all cases (G5, lowFreq, and novel) * The variant mapping step has the option of letting users select whether they want to report the bp distance between each identified intron variant and its nearby exon * The pipeline can deal with VCF files called by different SAMTools versions (0.1.18 and older ones) and also offers flexibility in dealing with vcf input files generated using SAMTools with two or three samples * The spreadsheet result file contains full protein sequences for both ref and alt alleles, which makes it easier for downstream protein structure/function analysis tools to take | single nucleotide polymorphism, amino acid, variant, annotation, exon, intron, mutation, next-generation sequencing, perl, downstream analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan Medical School; Michigan; USA |
PMID:24250114 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01922, biotools:snpaamapper | https://bio.tools/snpaamapper | SCR_002012 | SNPAAMapper - A SNP Amino Acid Mapping tool | 2026-09-19 12:55:50 | 0 | |||||
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skewer Resource Report Resource Website 10+ mentions |
skewer (RRID:SCR_001151) | skewer | data processing software, software application, software resource | Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences. | illumina, unix/linux, c++, adapter trimming, paired-end, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24925680 | Free, Available for download, Freely available | OMICS_02106, biotools:skewer | https://bio.tools/skewer, https://sources.debian.org/src/skewer/, https://github.com/relipmoc/skewer | SCR_001151 | skewer - A fast and sensitive adapter trimmer for illumina paired-end sequences | 2026-09-19 12:55:49 | 14 | |||||
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Mspire-Simulator Resource Report Resource Website 1+ mentions |
Mspire-Simulator (RRID:SCR_001431) | simulation software, software application, software resource, standalone software | A free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components. | standalone software, shotgun, proteomic, simulation software, bio.tools |
uses: mzML is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: Brigham Young University; Utah; USA |
PMID:24090032 | Free, Freely Available | biotools:mspire-simulator, OMICS_03359 | https://bio.tools/mspire-simulator | SCR_001431 | 2026-09-19 12:55:50 | 1 | |||||||
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HTqPCR Resource Report Resource Website 50+ mentions |
HTqPCR (RRID:SCR_003375) | HTqPCR | data processing software, software application, software resource | Software package for the analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs). | data import, differential expression, gene expression, microtitre plate assay, multiple comparison, preprocessing, quality control, visualization, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
PMID:19808880 | Free, Available for download, Freely available | biotools:htqpcr, OMICS_02314 | https://bio.tools/htqpcr | SCR_003375 | HTqPCR - Automated analysis of high-throughput qPCR data | 2026-09-19 12:55:52 | 74 | |||||
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NanoStringNorm Resource Report Resource Website 100+ mentions |
NanoStringNorm (RRID:SCR_003382) | NanoStringNorm | data processing software, software application, software resource | Software package for normalizing, diagnostics and visualization of NanoString nCounter data. Key features include an extensible environment for method comparison and new algorithm development, integrated gene and sample diagnostics, and facilitated downstream statistical analysis. | normalization, nanostring ncounter, mirna, mrna, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Ontario Institute for Cancer Research |
PMID:22513995 | Free, Available for download, Freely available | OMICS_02308, biotools:nanostringnorm | https://www.rdocumentation.org/packages/NanoStringNorm/versions/1.2.1.1/topics/NanoStringNorm | SCR_003382 | NanoStringNorm: Normalize NanoString miRNA and mRNA data | 2026-09-19 12:55:52 | 137 | |||||
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IMG System Resource Report Resource Website 100+ mentions |
IMG System (RRID:SCR_002965) | IMG, IMG/M | data or information resource, portal | Resource for analysis and annotation of genome and metagenome datasets in comprehensive comparative context. IMG provides users with tools for analyzing publicly available genome datasets and metagenome datasets. | microbiome, microbial genetics, genome and metagenome datasets analysis, genome and metagenome datasets, genome, metagenomics, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: Human Microbiome Project has parent organization: DOE Joint Genome Institute |
PMID:17932063 PMID:22086953 |
Free, Freely available | nif-0000-03010, OMICS_01478, SCR_014605, biotools:img_m | http://img.jgi.doe.gov/m, https://bio.tools/img_m | SCR_002965 | Integrated Microbial Genomes System | 2026-09-19 12:55:52 | 212 | |||||
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SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_007075) | data processing software, software application, software resource | A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options. | gene, gene expression, function, analysis, visualization, statistical analysis, windows, c#, gene function, chromosome location, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Gene Expression Omnibus |
PMID:14988116 | Free | nlx_149285, biotools:seqexpress | https://bio.tools/seqexpress | SCR_007075 | 2026-09-19 12:55:56 | 0 | |||||||
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RIKEN integrated database of mammals Resource Report Resource Website |
RIKEN integrated database of mammals (RRID:SCR_006890) | RIKEN integrated database of mammals | data or information resource, database, portal |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019. A database that integrates not only RIKEN''''s original large-scale mammalian databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists'''' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information. |
integration, network, standardization, biomedical, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Functional Annotation of the Mammalian Genome is related to: Cerebellar Development Transcriptome Database is related to: Ensembl is related to: Mouse Genome Informatics (MGI) is related to: OBO has parent organization: RIKEN Yokohama Institute; Kanagawa; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:21076152 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151886, biotools:riken | https://bio.tools/riken | SCR_006890 | 2026-09-19 12:55:56 | 0 | |||||
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epigenomix Resource Report Resource Website 1+ mentions |
epigenomix (RRID:SCR_006407) | epigenomix | data processing software, software application, software resource | Software package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types. | epigenetic, gene expression, microarray, histone modification, chip-seq, classification, differential expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24403540 | GNU Lesser General Public License, v3 | biotools:epigenomix, OMICS_02205 | https://bio.tools/epigenomix | SCR_006407 | epigenomix - Epigenetic and gene expression data normalization and integration with mixture models | 2026-09-19 12:55:55 | 2 | |||||
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SOAPaligner/soap2 Resource Report Resource Website 100+ mentions |
SOAPaligner/soap2 (RRID:SCR_005503) | SOAPaligner, SOAP2 | data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, alignment, short read, oligonucleotide, single-read, pair-end, resequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SOAP |
PMID:19497933 DOI:10.1093/bioinformatics/btn025 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:soap2 | https://bio.tools/soap2, https://sources.debian.org/src/soapaligner/ | SCR_005503 | 2026-09-19 12:55:54 | 325 | ||||||
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Pedigree-Draw Resource Report Resource Website 1+ mentions |
Pedigree-Draw (RRID:SCR_008302) | commercial organization, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software) | gene, genetic, genomic, macos, bio.tools |
is listed by: Genetic Analysis Software is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154520, OMICS_00213, SCR_010795 | SCR_008302 | PEDIGREE/DRAW | 2026-09-19 12:55:57 | 1 | ||||||||
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COILS: Prediction of Coiled Coil Regions in Proteins Resource Report Resource Website 100+ mentions |
COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) | data processing software, software application, software resource | COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. | software, prediction, database, sequence, coil, globular, protein, probability, bio.tools, FASEB list |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1126/science.252.5009.1162 | biotools:ncoils, OMICS_07850, nif-0000-30263 | https://bio.tools/ncoils, https://sources.debian.org/src/ncoils/ | https://sources.debian.org/src/ncoils/ | SCR_008440 | COILS Server | 2026-09-19 12:55:57 | 169 |
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