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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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LitMiner Resource Report Resource Website 1+ mentions |
LitMiner (RRID:SCR_008200) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The LitMiner software is a literature data-mining tool that facilitates the identification of major gene regulation key players related to a user-defined field of interest in PubMed abstracts. The prediction of gene-regulatory relationships is based on co-occurrence analysis of key terms within the abstracts. LitMiner predicts relationships between key terms from the biomedical domain in four categories (genes, chemical compounds, diseases and tissues). The usefulness of the LitMiner system has been demonstrated recently in a study that reconstructed disease-related regulatory networks by promoter modeling that was initiated by a LitMiner generated primary gene list. To overcome the limitations and to verify and improve the data, we developed WikiGene, a Wiki-based curation tool that allows revision of the data by expert users over the Internet. It is based on the annotation of key terms in article abstracts followed by statistical co-citation analysis of annotated key terms in order to predict relationships. Key terms belonging to four different categories are used for the annotation process: -Genes: Names of genes and gene products. Gene name recognition is based on Ensembl . Synonyms and aliases are resolved. -Chemical Compounds: Names of chemical compounds and their respective aliases. -Diseases and Phenotypes: Names of diseases and phenotypes -Tissues and Organs: Names of tissues and organs LitMiner uses a database of disease and phenotype terms for literature annotation. Currently, there are 2225 diseases or phenotypes, 801 tissues and organs, and 10477 compounds in the database. | gene, biomedical, chemical, compound, disease, identification, literature, medline interfaces, mining, modeling, phenotype, promoter, regulation, regulatory, relationship, tissue, tool, bio.tools |
is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21241, biotools:litminer | https://bio.tools/litminer | SCR_008200 | LitMiner | 2026-09-12 01:01:58 | 2 | |||||||
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Homologous Sequences in Ensembl Animal Genomes Resource Report Resource Website 1+ mentions |
Homologous Sequences in Ensembl Animal Genomes (RRID:SCR_008356) | HOMOLENS | data or information resource, database | Database of homologous genes from Ensembl organisms, structured under ACNUC sequence database management system. It allows to select sets of homologous genes among species, and to visualize multiple alignments and phylogenetic trees. It is possible to search for orthologous genes in a wide range of taxons. HOMOLENS is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generally, HOMOLENS gives an overall view of what is known about a peculiar gene family. Note that HOMOLENS is split into two databases on this server: HOMOLENS contains the protein sequences while HOMOLENSDNA contains the nucleotide sequences. Protein sequences of HOMOLENS have been generated by translating the CDS of HOMOLENSDNA and using associated cross-references to generate the annotations. | ensembl, evolution, gene, alignment, comparative, homologous, molecular, nucleotide, organism, phylogenetic, phylogeny, protein, sequence, specie, structure, taxon, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Claude Bernard University Lyon 1; Lyon; France |
biotools:homolens, nif-0000-25424 | https://bio.tools/homolens | SCR_008356 | 2026-09-12 01:01:59 | 3 | ||||||||
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Regulatory Sequence Analysis Tools Resource Report Resource Website 100+ mentions |
Regulatory Sequence Analysis Tools (RRID:SCR_008560) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Retrieve-ensembl-seq is included in the software suite regulatory sequence analysis tools (RSAT), allowing instant submission of retrieved sequences to further analysis tools. AVAILABILITY: retrieve-ensembl-seq is integrated in the RSAT suite: http://rsat.ulb.ac.be/rsat. Web site: http://rsat.ulb.ac.be/rsat/retrieve-ensembl-seq_form.cgi. Web services: http://rsat.ulb.ac.be/rsat/web_services/RSATWS.wsdl. Stand-alone distribution: freely available under an academic licence to download from the RSAT web site. The complete manual, a convenient tutorial and demos are available from the RSAT website. Additional help can be found on the RSAT public forum. | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Yeast Search for Transcriptional Regulators And Consensus Tracking |
DOI:10.1093/nar/gkv362 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:rsat, nif-0000-31437, OMICS_08097 | https://bio.tools/rsat | https://sources.debian.org/src/rsat/ | SCR_008560 | RSAT | 2026-09-12 01:02:00 | 108 | |||||
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Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) Resource Report Resource Website 10+ mentions |
Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) (RRID:SCR_008621) | SNPSpD | analysis service resource, data analysis service, production service resource, service resource | SNPSpD is a method of correcting for non-independance of single nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of LD between SNP''s. Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Queensland Institute of Medical Research |
National Health and MRC Australia 241916 | PMID:14997420 | biotools:snpspd, nif-0000-31985 | https://bio.tools/snpspd | http://genepi.qimr.edu.au/general/daleN/SNPSp | SCR_008621 | Single Nucleotide Polymorphism Spectral Decomposition | 2026-09-12 01:02:00 | 18 | ||||
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Webproanalyst Resource Report Resource Website |
Webproanalyst (RRID:SCR_008348) | analysis service resource, data analysis service, production service resource, service resource | WebProAnalyst provides web-accessible analysis for scanning the quantitative structure-activity relationships in protein families. It searches for a sequence region, whose substitutions are correlated with variations in the activities of a homologous protein set, the so-called activity modulating sites. WebProAnalyst allows users to search for the key physicochemical characteristics of the sites that affect the changes in protein activities. It enables the building of multiple linear regression and neural networks models that relate these characteristics to protein activities. WebProAnalyst implements multiple linear regression analysis, back propagation neural networks and the Structure-Activity Correlation/Determination Coefficient (SACC/SADC). A back propagation neural network is implemented as a two-layered network, one layer as input, the other as output (Rumelhart et al, 1986). WebProAnalyst uses alignment of amino acid sequences and data on protein activity (pK, Km, ED50, among others). The input data are the numerical values for the physicochemical characteristics of a site in the multiple alignment given by a slide window. The output data are the predicted activity values. The current version of WebProAnalyst handles a single activity for a single protein. The SACC/SADC may be defined as an estimate of the strongest multiple correlation between the physicochemical characteristics of a site in a multiple alignment and protein activities. The SACC/SADC coefficient makes possible the calculation of the possible highest correlation achievable for the quantitative relationship between the physicochemical properties of sites and protein activities. The SACC/SADC is a convenient means for an arrangement of positions by their functional significance. WebProAnalyst outputs a list of multiple alignment positions, the respective correlation values, also regression analysis parameters for the relationships between the amino acid physicochemical characteristics at these positions and the protein activity values. | family, functional, activity, alignment, amino acid, homologous, modulating site, neural, physicochemical, propagation, protein, quantitative, region, relationship, scan, sequence, structure, substitution, variation, bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-25212, biotools:webproanalyst | https://bio.tools/webproanalyst | SCR_008348 | Webproanalyst | 2026-09-12 01:01:59 | 0 | ||||||||
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GeneSeeker Resource Report Resource Website 1+ mentions |
GeneSeeker (RRID:SCR_008347) | data or information resource, database | The GeneSeeker allows you to search across different databases simultaneously, given a known human genetic location and expression/phenotypic pattern. The GeneSeeker returns any found gene names which are located on the specified location and expressed in the specified tissue. To search for more expression location in one search, just enter them in the textbox for the expression location and separate them with logical operators (and, or, not). You can specify as many tissues as you want, the program starts 20 queries simultaneously, and then waits for a query to finish before starting another query, to keep server loads to a minimum. You can also search only for expression, just leave the cytogenetic location fields blank, and do the query. If you only want to look for one cytogenetic location, only fill in the first location field, and the GeneSeeker will search with only this one. Housekeeping genes , found in Swissprot can be excluded, or genes that are to be excluded can be specified. Human chromosome localizations are translated with an oxford-grid to mouse chromosome localizations, and then submitted to the Mgd. Sponsors: GeneSeeker is a service provided by the Centre for Molecular and Biomolecular Informatics (CMBI). | expression, federated database, gene, genetic, biomolecular, chromosome, cytogenetic, database, human, localization, location, molecular, pattern, phenotypic, tissue, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Radboud University; Nijmegen; The Netherlands |
biotools:geneseeker, nif-0000-25211 | https://bio.tools/geneseeker | SCR_008347 | GeneSeeker | 2026-09-12 01:01:59 | 5 | ||||||||
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DNAtraffic Resource Report Resource Website |
DNAtraffic (RRID:SCR_008886) | DNAtraffic | data or information resource, database | DNAtraffic database is dedicated to be an unique comprehensive and richly annotated database of genome dynamics during the cell life. DNAtraffic contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling, DNA repair and damage response pathways from eight model organisms commonly used in the DNA-related study: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Escherichia coli and Arabidopsis thaliana. DNAtraffic contains comprehensive information on diseases related to the assembled human proteins. Database is richly annotated in the systemic information on the nomenclature, chemistry and structure of the DNA damage and drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA metabolism pathway analysis. Database includes illustrations of pathway, damage, protein and drug. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines it has to be extensively linked to numerous external data sources. Database represents the result of the manual annotation work aimed at making the DNAtraffic database much more useful for a wide range of systems biology applications. DNAtraffic database is freely available and can be queried by the name of DNA network process, DNA damage, protein, disease, and drug. | dna, cell cycle, genome, nomenclature, ontology, structure, function, protein, chromatin remodeling, dna repair, damage response pathway, pathway, damage, drug, annotation, disease, dna network process, dna damage, gene sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Polish Academy of Sciences Warsaw; Warsaw; Poland |
Norwegian Financial Mechanism PNRF-143-AI-1/07; Polish Ministry of Science and Higher Education N N301 165835 |
PMID:22110027 | Free | biotools:dnatraffic, nlx_151312 | https://bio.tools/dnatraffic | SCR_008886 | DNAtraffic database | 2026-09-12 01:02:02 | 0 | ||||
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SPIKE Resource Report Resource Website 100+ mentions |
SPIKE (RRID:SCR_010466) | SPIKE | data or information resource, database, service resource | Database of curated human signaling pathways with an associated interactive software tool for analysis and dynamic visualization of pathways. Individual pathway maps can be viewed and downloaded; the entire database may be browsed, or launched via a map viewer tool that allows dynamic visualization of the database and save networks in XGMML format that can be viewed in all generic XGMML viewers. Map Topics * Cell cycle progress and check points * DNA damage response * Programmed cell death related processes * Stress-activated transcription factors * Mitogen-activated protein kinase pathways * Immune response signaling * HEarSpike: hearing related pathways | visualization, analysis, cellular, signaling pathway, regulatory network, function, genomic, proteomic, cell cycle, dna damage, cell death, stress, transcription factor, mitogen, protein kinase, pathway, immune response, signaling, hearing, dna damage response, programmed cell death, development, ear, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: ConsensusPathDB has parent organization: Tel Aviv University; Ramat Aviv; Israel |
Cancer | A-T Children's Project ; Wolfson Foundation ; European Union FP7 ; Israel Science Foundation |
PMID:21097778 PMID:18289391 |
biotools:spike, nlx_157705 | https://bio.tools/spike | SCR_010466 | Signaling Pathway Integrated Knowledge Engine | 2026-09-12 01:02:03 | 131 | ||||
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NEBcutter Resource Report Resource Website 100+ mentions |
NEBcutter (RRID:SCR_010664) | analysis service resource, data analysis service, production service resource, service resource | This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once. By default, only enzymes available from NEB are used, but other sets may be chosen. Just enter your sequence and submit. Further options will appear with the output. The maximum size of the input file is 1 MByte, and the maximum sequence length is 300 KBases. NEBcutter produces a variety of outputs including restriction enzyme maps, theoretical digests and links into the restriction enzyme database, REBASE (http://rebase.neb.com/rebase/rebase.html). Importantly, its table of recognition sites is updated daily from REBASE and it marks all sites that are potentially affected by DNA methylation (Dam, Dcm, etc.). Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini. | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: New England Biolabs |
PMID:12824395 | biotools:nebcutter, nlx_71778 | https://bio.tools/nebcutter | SCR_010664 | 2026-09-12 01:02:05 | 151 | ||||||||
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omiRas Resource Report Resource Website 10+ mentions |
omiRas (RRID:SCR_010833) | omiRas | analysis service resource, data analysis service, production service resource, service resource | A web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23946503 | biotools:omiras, OMICS_00383 | https://bio.tools/omiras | SCR_010833 | 2026-09-12 01:02:06 | 14 | |||||||
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MutationTaster Resource Report Resource Website 1000+ mentions |
MutationTaster (RRID:SCR_010777) | MutationTaster | analysis service resource, data analysis service, production service resource, service resource | Evaluates disease-causing potential of sequence alterations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20676075 | Acknowledgement requested | biotools:mutation_taster, OMICS_00153 | https://bio.tools/mutation_taster | SCR_010777 | 2026-09-12 01:02:06 | 4781 | ||||||
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FINDbase Worldwide Resource Report Resource Website 10+ mentions |
FINDbase Worldwide (RRID:SCR_012744) | data or information resource, database | FINDbase Worldwide is an online repository of information about the frequency of different mutations leading to inherited disorders in various populations around the globe. Frequency data about 32 disorders, 25 genes within 98 populations covering 1226 mutations is now available. 28 curators worldwide contributed to this database containing data from 37 submissions. | genetic disorder, human mutation, inherited disorder, mutation pathogenesis, bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:findbase, nif-0000-02838 | https://bio.tools/findbase | SCR_012744 | FINDbase | 2026-09-12 01:02:08 | 13 | ||||||||
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CancerResource Resource Report Resource Website 1+ mentions |
CancerResource (RRID:SCR_011945) | data or information resource, database | Comprehensive database of cancer relevant proteins and compound interactions supported by experimental knowledge.Knowledgebase for drug-target relationships related to cancer as well as for supporting information or experimental data. | compound, drug, target gene, cancer relevant proteins, compound interactions, drug-target relationships, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Cancer | DFG ; European Union ; Federal Ministry of Education and Research BMBF ; International Research Training Group IRTG |
PMID:20952398 | Free, Freely available | biotools:cancerresource, OMICS_01576 | https://bio.tools/cancerresource | http://bioinf-data.charite.de/cancerresource/index.php?site=home | SCR_011945 | 2026-09-12 01:02:07 | 5 | ||||
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NHLBI Exome Sequencing Project (ESP) Resource Report Resource Website 1000+ mentions |
NHLBI Exome Sequencing Project (ESP) (RRID:SCR_012761) | EVS | data or information resource, database | The goal of the project is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by pioneering the application of next-generation sequencing of the protein coding regions of the human genome across diverse, richly-phenotyped populations and to share these datasets and findings with the scientific community to extend and enrich the diagnosis, management and treatment of heart, lung and blood disorders. The groups participating and collaborating in the NHLBI GO ESP include: Seattle GO - University of Washington, Seattle, WA Broad GO - Broad Institute of MIT and Harvard, Cambridge, MA WHISP GO - Ohio State University Medical Center, Columbus, OH Lung GO - University of Washington, Seattle, WA WashU GO - Washington University, St. Louis, MO Heart GO - University of Virginia Health System, Charlottesville, VA ChargeS GO - University of Texas Health Sciences Center at Houston | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
NHLBI | biotools:esp, nlx_156901, biotools:exome_variant_server | https://bio.tools/esp, https://bio.tools/exome_variant_server | SCR_012761 | Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP) | 2026-09-12 01:02:08 | 2231 | ||||||
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ComiR Resource Report Resource Website 10+ mentions |
ComiR (RRID:SCR_013023) | ComiR | analysis service resource, data analysis service, production service resource, service resource | Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data. | mirna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Pittsburgh; Pennsylvania; USA |
NLM ; Fondazione RiMED |
PMID:23703208 PMID:23284279 |
Acknowledgement requested | OMICS_00395, biotools:comir | https://bio.tools/comir | SCR_013023 | Combinatorial miRNA targeting, ComiR: Combinatorial miRNA target prediction tool, ComiR - Combinatorial miRNA target prediction tool | 2026-09-12 01:02:09 | 26 | ||||
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Fugu Genome Project Resource Report Resource Website 10+ mentions |
Fugu Genome Project (RRID:SCR_013014) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE,documented on August 16, 2019. Fugu genome is among the smallest vertebrate genomes and has proved to be a valuable reference genome for identifying genes and other functional elements such as regulatory elements in the human and other vertebrate genomes, and for understanding the structure and evolution of vertebrate genomes. This site presents version 4 of the Fugu genome, released in October 2004 by the International Fugu Genome Consortium. Fugu rubripes has a very compact genome, with less than 15 consisting of dispersed repetitive sequence, which makes it ideal for gene discovery. A draft sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002 using the ''whole-genome shotgun'' sequencing strategy. Fugu is the second vertebrate genome to be sequenced, the first being the human genome. This webpage presents the annotation made on the fourth assembly by the IMCB team using the Ensembl annotation pipeline. We are continuing with the gap filling work and linking of the scaffolds to obtain super-contigs. | element, evolution, fish, fugu, functional, gene, genome, human, pufferfish, regulatory, rubripes, structure, vertebrate, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Institute of Molecular and Cell Biology; Singapore; Singapore |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fugu-sg, nif-0000-20988 | https://bio.tools/fugu-sg | SCR_013014 | FGP | 2026-09-12 01:02:09 | 22 | |||||||
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GenoREAD Resource Report Resource Website |
GenoREAD (RRID:SCR_012007) | GenoREAD | analysis service resource, data analysis service, production service resource, service resource | A sequence verification pipeline where users can submit trace files to verify if a clone''s physical sequence matches its reference sequence. | clone, verification, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Virginia Bioinformatics Institute |
PMID:23042248 | Acknowledgement requested | OMICS_01823, biotools:genoread | https://bio.tools/genoread | SCR_012007 | GenoREAD - Sequencing Verification Pipeline | 2026-09-12 01:02:07 | 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 | 2026-09-12 01:00:52 | 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 | 2026-09-12 01:00:52 | 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 | 2026-09-12 01:00:54 | 74 |
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