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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Aroma.affymetrix Resource Report Resource Website 10+ mentions |
Aroma.affymetrix (RRID:SCR_010919) | Aroma.affymetrix | software resource | An R package for analyzing large Affymetrix data sets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00703, biotools:aroma.affymetrix | https://bio.tools/aroma.affymetrix | SCR_010919 | SciCrunch Registry | 2026-10-10 12:38:40 | 34 | ||||||||
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kmer-SVM Resource Report Resource Website 1+ mentions |
kmer-SVM (RRID:SCR_010882) | kmer-SVM | analysis service resource, data analysis service, production service resource, service resource, software resource | A webserver built on the Galaxy framework that enables the mining of sequence data for transcription factor binding sites. This tool suite was designed to aid in analysis of next-generation sequencing (NGS) data that uses a support vector machine (SVM) with kmer sequence features to identify predictive combinations of short transcription factor binding sites which determine the tissue specificity of the original NGS assay. While you may use datasets already available from Galaxy, you can upload your data using the ''Get Data'' Tool. The tool can upload data from a variety of locations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA has parent organization: Galaxy |
PMID:23771147 | Acknowledgement requested | OMICS_00484, biotools:kmer-svm | https://bio.tools/kmer-svm | SCR_010882 | SciCrunch Registry | 2026-10-10 12:38:20 | 3 | ||||||
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NURD Resource Report Resource Website 50+ mentions |
NURD (RRID:SCR_010988) | NURD | software resource | An algorithm to inference isoform expression., 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 | biotools:nurd, OMICS_01283 | https://bio.tools/nurd | SCR_010988 | SciCrunch Registry | 2026-10-10 12:38:42 | 72 | |||||||
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Gene3D Resource Report Resource Website 100+ mentions |
Gene3D (RRID:SCR_007672) | Gene3D | data access protocol, data or information resource, data repository, database, service resource, software resource, storage service resource, web service | A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes CATH domains from Protein Databank (PDB) structures and assigns them to the millions of protein sequences with no PDB structures using Hidden Markov models. Assigning a CATH superfamily to a region of a protein sequence gives information on the gross 3D structure of that region of the protein. CATH superfamilies have a limited set of functions and so the domain assignment provides some functional insights. Furthermore most proteins have several different domains in a specific order, so looking for proteins with a similar domain organization provides further functional insights. Strict confidence cut-offs are used to ensure the reliability of the domain assignments. Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | protein domain, protein, protein superfamily, hidden markov model, structural domain, genome, sequence, domain assignments, protein structure, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University College London; London; United Kingdom |
NIH ; Wellcome Trust ; European Union FP6 ENFIN LSHG-CT-2003-503265; European Union FP6 ENFIN LSHG-CT-2004-512092; European Union FP6 ENFIN LSHG-CT-2005-518254; DOE DE-AC02-065CH11357 |
PMID:19906693 PMID:18032434 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02877, biotools:gene3d | https://bio.tools/gene3d | SCR_007672 | SciCrunch Registry | Gene3D - Structures assigned to Genomes | 2026-10-10 12:37:51 | 272 | ||||
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AmpliconNoise Resource Report Resource Website 50+ mentions |
AmpliconNoise (RRID:SCR_007814) | AmpliconNoise | software resource | A collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
DOI:10.1186/1471-2105-12-38 | biotools:pyronoise, OMICS_01112 | https://bio.tools/pyronoise, https://sources.debian.org/src/anfo/ | SCR_007814 | SciCrunch Registry | 2026-10-10 12:37:55 | 91 | |||||||
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ALTree Resource Report Resource Website 1+ mentions |
ALTree (RRID:SCR_007562) | data analysis software, data processing software, software application, software resource | Software package to perform phylogeny based association and localization analysis.Used for association detection and localization of susceptibility sites using haplotype phylogenetic trees. Performs these two phylogeny-based analysis: tests association between candidate gene and disease; pinpoints markers (SNPs) that are putative disease susceptibility loci. | phylogeny based association, association detection, susceptibility sites, haplotype phylogenetic trees, gene, genetic, genomic |
is listed by: Genetic Analysis Software is listed by: Debian |
PMID:16595555 DOI:10.1093/bioinformatics/btl131 |
Free, Available for download, Freely available | OMICS_13032, nlx_154221 | https://sources.debian.org/src/altree/, https://gitlab.inria.fr/NGS/ALTree, | SCR_007562 | SciCrunch Registry | ALTREE | 2026-10-10 12:37:54 | 3 | ||||||
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Gene Expression Atlas Resource Report Resource Website 100+ mentions |
Gene Expression Atlas (RRID:SCR_007989) | atlas, data or information resource, database, expression atlas | Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. The EBI Gene Expression Atlas Blog discusses ideas, features and problems of creating a large scale meta-analytical atlas of gene expression from publicly available microarray data. Atlas REST API provides all the results available in the main web application in a pragmatic, easy to use form - simple HTTP GET queries as input and either JSON or XML formats as output. Gene Expression Atlas goals: 1. Provision of a statistically robust framework for integration of gene expression experiment results across different platforms at a meta-analytical level 2. A simple interface for identifying strong differential expression candidate genes in conditions of interest 3. Integration of ontologies for high quality annotation of gene and sample attributes 4. Construction of new gene expression summarized views, with a view to analysis of putative signaling pathway targets, discovery of correlated gene expression patterns and the identification of condition/tissue-specific patterns of gene expression. | expression, gene, annotation, assay, molecular neuroanatomy resource, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: ArrayExpress is related to: Experimental Factor Ontology has parent organization: European Bioinformatics Institute |
EMBL ; European Union FELICS ; European Union EMERALD |
nif-0000-06686, biotools:gxa_expt, r3d100010223, biotools:gene_expression_atlas | https://bio.tools/gxa_expt, https://bio.tools/gene_expression_atlas, https://doi.org/10.17616/R3Z888 | SCR_007989 | SciCrunch Registry | 2026-10-10 12:37:53 | 132 | ||||||||
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Variant Effect Predictor Resource Report Resource Website 1000+ mentions |
Variant Effect Predictor (RRID:SCR_007931) | VEP | analysis service resource, data analysis service, production service resource, service resource, software resource | Data analysis service to predict the functional consequences of known and unknown variants. | perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ensembl |
biotools:ensembl_variant_effect_predictor | https://bio.tools/ensembl_variant_effect_predictor | SCR_007931 | SciCrunch Registry | Ve!P | 2026-10-10 12:37:54 | 2073 | |||||||
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eTBlast Resource Report Resource Website 1+ mentions |
eTBlast (RRID:SCR_008188) | eTBlast | data or information resource, database, narrative resource, service resource | eTBLAST is a unique search engine for searching biomedical literature. Our service is very different from PubMed. While PubMed searches for keywords, our search engine lets you input an entire paragraph and returns MEDLINE abstracts that are similar to it. This is something like PubMed''s Related Articles feature, only better because it runs on your unique set of interests. For example, input the abstract of an unpublished paper or a grant proposal into our engine, and with the touch of a button you''ll be able to find every abstract in MEDLINE dealing with your topic. No more guessing whether your set of keywords has found all the right papers. No more sorting through hundreds of papers you don''t care about to find the handful you were looking for--our search engine does it for you. When most people use PubMed to search MEDLINE they pick one or two keywords to describe their topic, then browse through a long list of results. When they find a paper that looks interesting they click on its Related Articles, in hopes of finding more papers like that one. If they find another relevant paper, they explore it''s related articles--and so on. This process of culling long lists of documents by hand makes literature searching tedious and time consuming. We make it easier for you by providing better results the first time, and then allowing you to automatically combine the papers you care about for a second round. Our Iterate feature allows you to checkmark the abstracts you found interesting in the first round and combine them all to create a new query. It''s like rolling several Related Articles lists into one. * We sort our results by relevance, while PubMed sorts by date. * We save you the time and effort of creating a complicated query. * We let you iterate your search over several good papers to narrow your focus. * We provide you the full MEDLINE abstract in our results, and a link to the PubMed page. * We can send your results straight to your email so you never lose a reference or forget where you found it. * This absolutely free service is provided by the University of Texas Southwestern Medical Center. No registration necessary! | biomedical, literature, medline interfaces, paper, publish, search engine, unpublished, journal, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA |
Hudson Foundation ; P.O'B. Montgomery Distinguished Chair |
PMID:16926219 | biotools:etblast, nif-0000-21148 | https://bio.tools/etblast | http://invention.swmed.edu/etblast/index.shtml | SCR_008188 | SciCrunch Registry | eTBLAST: a text-similarity based search engine | 2026-10-10 12:37:55 | 5 | ||||
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Network Analysis, Visualization and Graphing TORonto Resource Report Resource Website 50+ mentions |
Network Analysis, Visualization and Graphing TORonto (RRID:SCR_008373) | NAViGaTOR | d visualization software, data processing software, data visualization software, software application, software resource | A software package for visualizing and analyzing protein-protein interaction networks. NAViGaTOR can query OPHID / I2D - online databases of interaction data - and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI). NAViGaTOR can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems. NAViGaTOR is written in Java and uses JOGL (Java bindings for OpenGL) to support scalability, highlighting or suppressing of information, and other advanced graphic approaches. | fly, algorithm, capacity, graphical, graphing, human, interaction, interactome, intersection, mouse, network, node, protein, proteomic, rat, worm, yeast, graphing application, 2d visualization, 3d visualization, visualization, biological network, protein-protein interaction, gene, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Genomics Institute ; Canada Research Chair Program ; Ontario Research Fund Research Excellence ; Canada Foundation for Innovation 12301; Canada Foundation for Innovation 203383 |
PMID:19837718 | Freely-downloadable for academic and not-for-profit institutions | nif-0000-25610, biotools:navigator | https://bio.tools/navigator | SCR_008373 | SciCrunch Registry | NAViGaTOR - Network Analysis Visualization and Graphing TORonto, NAViGaTOR - Network Analysis Visualization & Graphing TORonto | 2026-10-10 12:38:19 | 55 | ||||
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EMBOSS Resource Report Resource Website 1000+ mentions |
EMBOSS (RRID:SCR_008493) | EMBOSS | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software analysis package for molecular biology community. Automatically copes with data in variety of formats and allows transparent retrieval of sequence data from web. Libraries are provided with package. Provides toolkit for creating bioinformatics applications or workflows. Provides set of sequence analysis programs. Provided programs cover areas such as sequence alignment, rapid database searching with sequence patterns, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis for small genomes, rapid identification of sequence patterns in large scale sequence sets, and presentation tools for publication. | FASEB list |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: BioExtract is related to: pepwheel |
DOI:10.1016/S0168-9525(00)02024-2 | Free, Freely available | OMICS_21165, nif-0000-30488 | https://sources.debian.org/src/emboss/ | http://www.emboss.org | SCR_008493 | SciCrunch Registry | The European Molecular Biology Open Software Suite, European Molecular Biology Open Software Suite | 2026-10-10 12:38:05 | 4742 | ||||
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Vienna RNA Resource Report Resource Website 100+ mentions |
Vienna RNA (RRID:SCR_008550) | data or information resource, database, software resource | This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI web server. With the 1st of May 2009 we updated our servers to the Vienna RNA package version 1.8.2! The Vienna RNA Servers: * RNAfold server predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences. * RNAalifold server predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment. * RNAinverse server allows you to design RNA sequences for any desired target secondary structure. * RNAcofold server allows you to predict the secondary structure of a dimer. * RNAup server allows you to predict the accessibility of a target region. * LocARNA server generates structural alignments from a set of sequences. In collaboration with the Bioinformatics Group Freiburg. * barriers server allows you to get insights into RNA folding kinetics. * RNAz server will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. * Structure conservation analysis server will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments. * RNAstrand server allows you to predict the reading direction of evolutionarily conserved RNA secondary structures. * RNAxs server assists you in siRNA design. * Bcheck predicts rnpB genes Downloads Get the Source code for: * the Vienna RNA Package, our basic RNA secondary structure analysis software. * The ALIDOT package for finding conserved structure motifs (add-on) * The barriers program for analysis of RNA folding landscapes. Databases * Atlas of conserved Viral RNA Structures found by ALIDOT | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ANNOgesic has parent organization: University of Vienna; Vienna; Austria |
DOI:10.1186/1748-7188-6-26 | biotools:vienna_rna_package, nif-0000-31411, OMICS_09351 | https://bio.tools/vienna_rna_package, https://sources.debian.org/src/vienna-rna/ | SCR_008550 | SciCrunch Registry | Vienna RNA | 2026-10-10 12:38:00 | 425 | |||||||
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tRNAscan-SE Resource Report Resource Website 1000+ mentions |
tRNAscan-SE (RRID:SCR_008637) | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | Web server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file). | bio.tools, tRNA genes, genomic sequence |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
PMID:15980563 PMID:9023104 DOI:10.1093/nar/25.5.0955 |
Free, Freely available | SCR_010835, OMICS_00385, nif-0000-32031, biotools:trnascan-se | https://bio.tools/trnascan-se, https://sources.debian.org/src/trnascan-se/ | SCR_008637 | SciCrunch Registry | Lowe Lab tRNAscan-SE | 2026-10-10 12:38:21 | 2855 | ||||||
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STEPS Resource Report Resource Website 100+ mentions |
STEPS (RRID:SCR_008742) | STEPS | simulation software, software application, software resource | STEPS is a package for exact stochastic simulation of reaction-diffusion systems in realistic, complex 3D geometries. Our core simulation algorithm is an efficient implementation of a variation on Gillespie''s SSA, extended to deal with diffusion of molecules over the elements of a 3D tetrahedral mesh. While it was mainly developed for simulating detailed models of neuronal signaling pathways in dendrites and around synapses, it is a general tool and can be used for studying any biochemical pathway in which spatial gradients and morphology are thought to play a role. We have implemented STEPS as a set of Python modules, which means STEPS users can use Python scripts to control all aspects of setting up the model, generating a mesh, controlling the simulation and generating and analyzing output. The core computational routines are still implemented as C/C++ extension modules for maximal speed of execution. | reaction-diffusion, stochastic, signaling, molecular, python, software, simulator, reaction kinetics, 3d diffusion, signaling pathway, scripting, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Okinawa Institute of Science and Technology has parent organization: University of Antwerp; Antwerp; Belgium |
GOA ; UA Belgium ; Human Frontier Science Program ; Okinawa Institute of Science and Technology |
biotools:steps, nlx_143852 | https://bio.tools/steps | http://steps.sourceforge.net/STEPS/Home.html | SCR_008742 | SciCrunch Registry | STochastic Engine For Pathway Simulation | 2026-10-10 12:38:02 | 342 | |||||
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Eukaryote Genes Resource Report Resource Website 10+ mentions |
Eukaryote Genes (RRID:SCR_008617) | data or information resource, database | Provides summary of gene and genomic information from eukaryotic organism databases. This includes gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information, links to extended gene information. | eukaryote, eukaryotic gene ontology, eukaryotic genome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Indiana University; Indiana; USA |
Indiana University Center for Genomics and Bioinformatics ; NSF DBI 0090782; NSF DBI 9982851 |
Free, Freely available | nif-0000-31969, biotools:eugenes, SCR_013197, nif-0000-02818 | https://bio.tools/eugenes | SCR_008617 | SciCrunch Registry | euGenes | 2026-10-10 12:38:21 | 17 | ||||||
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RUM Resource Report Resource Website 1+ mentions |
RUM (RRID:SCR_008818) | RUM | software resource | An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
OMICS_01249, biotools:rum | https://bio.tools/rum, https://github.com/itmat/rum/wiki | SCR_008818 | SciCrunch Registry | Rna seq Unified Mapper | 2026-10-10 12:38:07 | 7 | |||||||
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QuasiRecomb Resource Report Resource Website 10+ mentions |
QuasiRecomb (RRID:SCR_008812) | QuasiRecomb | software resource | A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. | haplotype, next-generation sequencing, virus, parameter, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23383997 | OMICS_00229, biotools:quasirecomb | https://bio.tools/quasirecomb | SCR_008812 | SciCrunch Registry | QuasiRecomb - Probabilistic inference of viral Quasispecies | 2026-10-10 12:38:11 | 33 | ||||||
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XPN Resource Report Resource Website 1+ mentions |
XPN (RRID:SCR_008845) | XPN | software resource | Merging Two Gene Expression Studies via Cross Platform Normalization. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
OMICS_00863, biotools:xpn | https://bio.tools/xpn | SCR_008845 | SciCrunch Registry | 2026-10-10 12:38:07 | 2 | ||||||||
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MuSiC Resource Report Resource Website 100+ mentions |
MuSiC (RRID:SCR_008792) | MuSiC | software resource | A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical 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: Washington University in St. Louis; Missouri; USA |
PMID:22759861 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:MuSiC2, OMICS_00152 | https://bio.tools/MuSiC2, https://github.com/ding-lab/MuSiC2/blob/master/README.md | SCR_008792 | SciCrunch Registry | Mutational Significance In Cancer | 2026-10-10 12:38:11 | 485 | |||||
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GMAP Resource Report Resource Website 500+ mentions |
GMAP (RRID:SCR_008992) | GMAP | alignment software, data processing software, image analysis software, software application, software resource, source code | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A software program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing. | mrna, est sequence, expressed sequence tag, sequence, cdna sequence, genome, cdna, bio.tools |
is used by: deFuse is listed by: Debian is listed by: bio.tools has parent organization: Genentech |
PMID:15728110 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15072, biotools:gmap, nlx_152505 | https://bio.tools/gmap, https://sources.debian.org/src/gmap/ | SCR_008992 | SciCrunch Registry | 2026-10-10 12:38:08 | 599 |
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