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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GFINDer: Genome Function INtegrated Discoverer Resource Report Resource Website 1+ mentions |
GFINDer: Genome Function INtegrated Discoverer (RRID:SCR_008868) | GFINDer | data analysis service, production service resource, analysis service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 16, 2019. Multi-database system providing large-scale lists of user-classified sequence identifiers with genome-scale biological information and functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves updated annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list, and calculates statistical significance values for each category. Moreover, GFINDer enables to functionally classify genes according to mined functional categories and to statistically analyze the obtained classifications, aiding in better interpreting microarray experiment results. | annotation, statistical analysis, mining, genome, function, sequence, functional profile, gene, microarray, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Polytechnic University of Milan; Milan; Italy |
PMID:15980570 PMID:15215397 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149256, biotools:gfinder | https://www.hsls.pitt.edu/obrc/index.php?page=URL1098209538, https://bio.tools/gfinder | SCR_008868 | Genome Function INtegrated Discoverer, Genome Function INtegrated Discoverer (GFINDer) | 2026-08-06 09:27:14 | 1 | |||||
|
MicroSNiPer Resource Report Resource Website 10+ mentions |
MicroSNiPer (RRID:SCR_009880) | MicroSNiPer | data analysis service, production service resource, analysis service resource, service resource | A web-based application which predicts the impact of a SNP on putative microRNA targets. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: National Institute of Mental Health |
PMID:20809528 | biotools:microsniper, OMICS_00388 | https://bio.tools/microsniper | SCR_009880 | 2026-08-06 09:27:24 | 18 | |||||||
|
Phylogeny.fr Resource Report Resource Website 500+ mentions |
Phylogeny.fr (RRID:SCR_010266) | database, data or information resource | A free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
PMID:18424797 | nlx_156923, biotools:phylogeny.fr | https://bio.tools/phylogeny.fr | SCR_010266 | 2026-08-06 09:27:30 | 667 | ||||||||
|
mirTools Resource Report Resource Website 10+ mentions |
mirTools (RRID:SCR_009701) | mirTools | data analysis service, production service resource, analysis service resource, service resource | A comprehensive web server developed to allow researchers to comprehensively characterize small RNA transcriptome. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23778453 | OMICS_00365, biotools:mirtools | https://bio.tools/mirtools | SCR_009701 | mirTools 2.0 | 2026-08-06 09:27:19 | 13 | ||||||
|
Hippocampome.org Resource Report Resource Website 10+ mentions |
Hippocampome.org (RRID:SCR_009023) | Hippocampome | database, data or information resource | A curated knowledge base of the circuitry of the hippocampus of normal adult, or adolescent, rodents at the mesoscopic level of neuronal types. Knowledge concerning dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex is distilled from published evidence and is continuously updated as new information becomes available. Each reported neuronal property is documented with a pointer to, and excerpt from, relevant published evidence, such as citation quotes or illustrations. Please note: This is an alpha-testing site. The content is still being vetted for accuracy and has not yet undergone peer-review. As such, it may contain inaccuracies and should not (yet) be trusted as a scholarly resource. The content does not yet appear uniformly across all combinations of browsers and screen resolutions. | interneuron, classification, neuroinformatics, network, hippocampus, neuron, property, morphology, molecular marker, electrophysiology, adult, adolescent, dentate gyrus, ca3, ca2, ca1, subiculum, entorhinal cortex, bio.tools |
is used by: BICCN is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: George Mason University; Virginia; USA |
Normal | Air Force Office of Scientific Research ; Office of Naval Research MURI N00014-10-1-0198; NINDS R01NS39600; NINDS R21NS58816 |
Except otherwise noted, Creative Commons Attribution-ShareAlike License | nlx_152892, biotools:Hippocampome.org | http://www.nitrc.org/projects/hippocampome, https://bio.tools/Hippocampome.org | SCR_009023 | Hippocampome Portal | 2026-08-06 09:27:16 | 32 | ||||
|
T-Coffee Resource Report Resource Website 1000+ mentions |
T-Coffee (RRID:SCR_011818) | T-Coffee | data analysis service, production service resource, analysis service resource, service resource | A multiple sequence alignment server which can align Protein, DNA and RNA sequences. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:10964570 DOI:10.1006/jmbi.2000.4042 |
biotools:tcoffee, OMICS_00989 | https://bio.tools/tcoffee, https://sources.debian.org/src/t-coffee/ | SCR_011818 | T-Coffee: Aligns DNA RNA or Proteins using the default T-Coffee | 2026-08-06 09:27:49 | 1121 | ||||||
|
DIANA-LncBase Resource Report Resource Website 100+ mentions |
DIANA-LncBase (RRID:SCR_010840) | LncBase | database, data or information resource | Database that hosts elaborated information for both predicted and experimentally verified, miRNA-lncRNA interactions. The database consists of two distinct modules. The Experimental Module contains detailed information for more than 5,000 interactions, between 2,958 lncRNAs and 120 miRNAs, ranging from miRNA and lncRNA related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. The Prediction Module, which is based on the latest version of DIANA-microT target prediction algorithm (DIANA-microT-CDS), contains detailed information for more than 10 million interactions, between 56,097 lncRNAs and 3,078 miRNAs, ranging from miRNA and lncRNA related details to specific information regarding their interaction sites, graphical representation of their binding and the predicted score. This module exhibits a unique feature for searching the database. Users are able to add genomic locations to their queries thus browsing every miRNA-lncRNA interaction that has at least one MRE located inside the queried locus. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23193281 | biotools:diana-lncbase, OMICS_00396 | https://bio.tools/diana-lncbase | SCR_010840 | 2026-08-06 09:27:40 | 161 | |||||||
|
ProbCons Resource Report Resource Website 100+ mentions |
ProbCons (RRID:SCR_011813) | ProbCons | data analysis service, production service resource, analysis service resource, service resource | Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Stanford University; Stanford; California |
PMID:15687296 DOI:10.1101/gr.2821705 |
OMICS_00986, biotools:probcons | https://bio.tools/probcons, https://sources.debian.org/src/probcons/ | SCR_011813 | ProbCons: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences | 2026-08-06 09:27:48 | 106 | ||||||
|
FGENESH Resource Report Resource Website 100+ mentions |
FGENESH (RRID:SCR_011928) | FGENESH | data analysis service, production service resource, analysis service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10,2020. Data analysis service for Hidden Markov Model (HMM)-based gene structure prediction (multiple genes, both chains). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fgenesh, OMICS_01483 | https://bio.tools/fgenesh | SCR_011928 | 2026-08-06 09:27:48 | 330 | |||||||
|
RACE Resource Report Resource Website 100+ mentions |
RACE (RRID:SCR_010950) | RACE | data analysis service, production service resource, analysis service resource, service resource | A collection of web tools designed to assist with the analysis of DNA microarray data and results. RACE performs probe level data preprocessing, quality checks, normalization, and visualization for Affymetrix GeneChips. In addition, it performs clustering and differential analysis of normalized expression levels or ratios for arbitrary platforms, and estimates the false discovery rates in lists of potentially regulated genes. A Gene Ontology (GO)-term analysis assists in the biological interpretation of gene lists. The user can customize each analysis request; upon submission the analysis is executed in a fully automated way., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | dna microarray, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Lausanne; Lausanne; Switzerland |
PMID:15980552 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00777, biotools:race | https://bio.tools/race | SCR_010950 | Remote Analysis Computation for gene Expression data | 2026-08-06 09:27:41 | 357 | |||||
|
HSLPred Resource Report Resource Website |
HSLPred (RRID:SCR_011972) | HSLPred | data analysis service, production service resource, analysis service resource, service resource | A support vector machine (SVM)-based method for the prediction of 4 major subcellular localization (cytoplasm, mitochondrial, nuclear and plasma membrane) of human proteins using various features such as i) amino acid composition, ii) dipeptide composition and iii) evolutionary information of proteins. | subcellular localization, protein, support vector machine, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Institute of Microbial Technology; Chandigarh; India |
PMID:15647269 | Acknowledgement requested | biotools:hslpred, OMICS_01622 | https://bio.tools/hslpred | SCR_011972 | HSLPred - A SVM-based Method for Subcellular Localization of Human Proteins | 2026-08-06 09:27:50 | 0 | |||||
|
Pscan-ChIP Resource Report Resource Website 1+ mentions |
Pscan-ChIP (RRID:SCR_010885) | Pscan-ChIP | data analysis service, production service resource, analysis service resource, service resource | Web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23748563 DOI:10.1093/nar/gkt448 |
biotools:pscanchip, OMICS_00490 | https://bio.tools/pscanchip, https://sources.debian.org/src/pscan-chip/ | SCR_010885 | 2026-08-06 09:27:45 | 5 | |||||||
|
CUPSAT Resource Report Resource Website 50+ mentions |
CUPSAT (RRID:SCR_010773) | CUPSAT | data analysis service, production service resource, analysis service resource, service resource | A tool to predict changes in protein stability upon point mutations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:16845001 | biotools:cupsat, OMICS_00128 | https://bio.tools/cupsat | SCR_010773 | Cologne University Protein Stability Analysis Tool, CUPSAT: Cologne University Protein Stability Analysis Tool | 2026-08-06 09:27:44 | 74 | ||||||
|
LS-SNP/PDB Resource Report Resource Website 1+ mentions |
LS-SNP/PDB (RRID:SCR_010774) | LS-SNP/PDB | data analysis service, production service resource, analysis service resource, service resource | A web tool for genome-wide annotation of human SNPs. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA |
OMICS_00131, biotools:ls-snp | https://bio.tools/ls-snp | SCR_010774 | 2026-08-06 09:27:40 | 3 | ||||||||
|
Vector Alignment Search Tool Resource Report Resource Website 10+ mentions |
Vector Alignment Search Tool (RRID:SCR_010655) | VAST | production service resource, analysis service resource, service resource | VAST is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison. Related structures for every structure in MMDB are pre-computed using VAST and accessible via links on the MMDB Structure Summary pages. The VAST Search page also allows you to compare the coordinates of a newly resolved structure in PDB format against all structures in MMDB to find its neighbors. Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the more than 87,804 domains in MMDB is compared to every other one. From the MMDB Structure summary pages, retrieved via Entrez, structure neighbors are available for protein chains and individual structural domains. If you already know a PDB/MMDB-Id you can try this at once, using the input form in the right column. VAST Search is a service that allows searching for structural neighbors starting with a set of 3D-coordinates specified by the user. This service is meant to be used with newly determined protein structures that are not yet part of MMDB. Structure neighbors for proteins already in MMDB have been pre-computed and can simply be looked up from MMDB''s Structure summary pages! | gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: NCBI Structure has parent organization: NCBI |
PMID:8804824 PMID:8710828 |
nlx_68740, biotools:vast | https://bio.tools/vast | SCR_010655 | Vector Alignment Search Tool (VAST) | 2026-08-06 09:27:42 | 17 | ||||||
|
PlantTFcat Resource Report Resource Website 10+ mentions |
PlantTFcat (RRID:SCR_010898) | PlantTFcat | data analysis service, production service resource, analysis service resource, service resource | A web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by systematically analyzing InterProScan domain patterns in protein sequences., 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: Samuel Roberts Noble Foundation |
PMID:24219505 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:planttfcat, OMICS_00559 | https://bio.tools/planttfcat | SCR_010898 | PlantTFcat: An Online Plant Transcription Factor and Transcriptional Regulator Categorization and Analysis Tool | 2026-08-06 09:27:45 | 44 | |||||
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ArrayPipe Resource Report Resource Website 10+ mentions |
ArrayPipe (RRID:SCR_010934) | ArrayPipe | data analysis service, production service resource, analysis service resource, service resource | A flexible tool for visualizing and analyzing your two-colour microarray slides. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00744, biotools:arraypipe | https://bio.tools/arraypipe | SCR_010934 | 2026-08-06 09:27:41 | 15 | ||||||||
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PREDDIMER Resource Report Resource Website 10+ mentions |
PREDDIMER (RRID:SCR_011963) | PREDDIMER | data analysis service, production service resource, analysis service resource, service resource | Prediction tool to reconstruct putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal alpha-helices. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24202542 | Free | OMICS_01614, biotools:preddimer | https://bio.tools/preddimer | SCR_011963 | PREDDIMER - Prediction tool for an ensemble of transmembrane ?-helical dimer conformations | 2026-08-06 09:27:50 | 15 | |||||
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HH-suite Resource Report Resource Website 10+ mentions |
HH-suite (RRID:SCR_016133) | sequence analysis software, software resource, data analysis software, software toolkit, data processing software, software application | Software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). Used for sequence-based protein function and structure prediction what depends on sequence-search sensitivity and accuracy of the resulting sequence alignments. | protein, sensitive sequence search, pairwise alignment, multiple database, homologous structure, prediction, modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
the Deutsche Forschungsgemeinschaft grant SFB646; Ludwig-Maximilians Universität Munich ; Excellence Initiative of the Bundesministerium für Bildung und Forschung |
DOI:10.1186/s12859-019-3019-7 | Free, Available for download, Freely available | biotools:hh-suite | https://bio.tools/hh-suite | http://toolkit.genzentrum.lmu.de/sections/search | SCR_016133 | 2026-08-06 09:28:46 | 49 | |||||
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DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | software resource, software tool, data analysis software, data processing software, software application | Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. | differential, gene, expression, analysis, binominal, distribution, RNA-seq data, Bioconductor, bio.tools |
is used by: Glimma is used by: TEtranscripts is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SARTools works with: tximport |
International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337; European Union’s 7th Framework Programme |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2, https://bio.tools/deseq2 | SCR_015687 | 2026-08-06 09:28:42 | 43994 |
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