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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ExpressYourself Resource Report Resource Website |
ExpressYourself (RRID:SCR_008881) | ExpressYourself | production service resource, data analysis service, service resource, analysis service resource | A fully integrated platform for processing microarray data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00755, biotools:expressyourself | https://bio.tools/expressyourself | SCR_008881 | ExpressYourself: microarray data processing platform, Express Yourself, Express Yourself: microarray data processing platform | 2026-08-02 09:05:32 | 0 | |||||||
|
miRNEST Resource Report Resource Website 1+ mentions |
miRNEST (RRID:SCR_008907) | miRNEST | database, data or information resource | A database of animal, plant and virus microRNA data maintained at the University of Poznan. The database provides: * 9980 miRNA candiates from 420 animal and plant species predicted in Expressed Sequence Tags * predicted targets for plant candidates * RNA-seq reads mapped to candidates from 29 species * external data from 12 databases that includes sequences, polymorphism, expression and regulation. miRNEST 1.0, it contains miRNA from 563 animals, plants and viruses plant species. | microrna, expressed sequence tag, rna-seq read, sequence, polymorphism, mirna sequence, small rna sequence, single nucleotide polymorphism, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Adam Mickiewicz University in Poznan; Poznan; Poland |
European Social Fund ; Adam Mickiewicz University PBWB-08/2011; Polish Ministry of Science and Higher Education N N301 160935; Polish Ministry of Science and Higher Education N N516 441938 |
PMID:22135287 | nlx_151465, biotools:mirnest | http://mirnest.amu.edu.pl, https://bio.tools/mirnest | SCR_008907 | miRNEST - a database of animal and plant microRNAs | 2026-08-02 09:05:46 | 3 | |||||
|
MicroSNiPer Resource Report Resource Website 10+ mentions |
MicroSNiPer (RRID:SCR_009880) | MicroSNiPer | production service resource, data analysis service, service resource, analysis 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 | 2026-08-02 09:05:52 | 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 | 2026-08-02 09:05:38 | 667 | ||||||||
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hiPathDB - human integrated Pathway DB with facile visualization Resource Report Resource Website 1+ mentions |
hiPathDB - human integrated Pathway DB with facile visualization (RRID:SCR_008900) | hiPathDB | database, data or information resource | hiPathDB is an integrated pathway database that combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta and KEGG. In total, it includes 1661 pathways consisting of 8976 distinct physical entities. (2010.03.09) hiPathDB provides two different types of integration. The pathway-level integration, conceptually a simple collection of individual pathways, was achieved by devising an elaborate model that takes distinct features of four databases into account and subsequently reformatting all pathways in accordance with our model. The entity-level integration creates a single unified pathway that encompasses all pathways by merging common components. Even though the detailed molecular-level information such as complex formation or post-translational modifications tends to be lost, such integration makes it possible to investigate signaling network over the entire pathways and allows identification of pathway cross-talks. Another strong merit of hiPathDB is the built-in pathway visualization module that supports explorative studies of complex networks in an interactive fashion. The layout algorithm is optimized for virtually automatic visualization of the pathways. | pathway, gene, compound, interaction, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: BioCarta Pathways is related to: Reactome is related to: Pathway Interaction Database has parent organization: Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea |
Ewha Womans University; Seoul; Korea ; Korean Ministry of Education Science and Technology 2011-000232; Korean Ministry of Education Science and Technology 2011-0019745; Korean Ministry of Education Science and Technology R15-2006-020 |
PMID:22123737 | nlx_151413, biotools:hipathdb | https://bio.tools/hipathdb | SCR_008900 | Human Integrated Pathway Database | 2026-08-02 09:05:32 | 3 | |||||
|
GFINDer: Genome Function INtegrated Discoverer Resource Report Resource Website 1+ mentions |
GFINDer: Genome Function INtegrated Discoverer (RRID:SCR_008868) | GFINDer | production service resource, data analysis service, service resource, analysis 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) | 2026-08-02 09:05:45 | 1 | |||||
|
mirTools Resource Report Resource Website 10+ mentions |
mirTools (RRID:SCR_009701) | mirTools | production service resource, data analysis service, service resource, analysis 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 | 2026-08-02 09:05:39 | 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 | 2026-08-02 09:05:49 | 32 | ||||
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AceDB Resource Report Resource Website 10+ mentions |
AceDB (RRID:SCR_010671) | database, data or information resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software genome database management system. | genome database management system, genome database, management system, |
is listed by: Debian is listed by: OMICtools is related to: ESTHER has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
DOI:10.1109/5992.764215 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_75315, OMICS_15828 | https://sources.debian.org/src/acedb-other/ | SCR_010671 | A C. elegans DataBase | 2026-08-02 09:05:57 | 12 | ||||||
|
Vector Alignment Search Tool Resource Report Resource Website 10+ mentions |
Vector Alignment Search Tool (RRID:SCR_010655) | VAST | production service resource, service resource, analysis 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) | 2026-08-02 09:05:45 | 17 | ||||||
|
T-Coffee Resource Report Resource Website 1000+ mentions |
T-Coffee (RRID:SCR_011818) | T-Coffee | production service resource, data analysis service, service resource, analysis 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 | 2026-08-02 09:05:55 | 1121 | ||||||
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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 | 2026-08-02 09:05:59 | 161 | |||||||
|
ProbCons Resource Report Resource Website 100+ mentions |
ProbCons (RRID:SCR_011813) | ProbCons | production service resource, data analysis service, service resource, analysis 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 | 2026-08-02 09:06:03 | 106 | ||||||
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Genome Database for Rosaceae Resource Report Resource Website 100+ mentions |
Genome Database for Rosaceae (RRID:SCR_012756) | database, data or information resource | GDR is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, annotated EST databases of apple, peach, almond, cherry, rose, raspberry and strawberry, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, ORFs, Gene Ontology and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. We continue to add Rosaceae map data to CMap, a web-based tool that allows users to view comparisons of genetic and physical maps. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm, search their sequences for microsatellites using the SSR server or assemble their ESTs using the CAP3 Server. | est, genome sequence, rosaceae, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Washington State University; Washington; USA |
nif-0000-02896, biotools:gdr | https://bio.tools/gdr | http://www.bioinfo.wsu.edu/gdr/ | SCR_012756 | GDR | 2026-08-02 09:06:02 | 486 | |||||||
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FGENESH Resource Report Resource Website 100+ mentions |
FGENESH (RRID:SCR_011928) | FGENESH | production service resource, data analysis service, service resource, analysis 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 | 2026-08-02 09:05:55 | 330 | |||||||
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RACE Resource Report Resource Website 100+ mentions |
RACE (RRID:SCR_010950) | RACE | production service resource, data analysis service, service resource, analysis 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 | 2026-08-02 09:05:59 | 357 | |||||
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HSLPred Resource Report Resource Website |
HSLPred (RRID:SCR_011972) | HSLPred | production service resource, data analysis service, service resource, analysis 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 | 2026-08-02 09:06:04 | 0 | |||||
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Pscan-ChIP Resource Report Resource Website 1+ mentions |
Pscan-ChIP (RRID:SCR_010885) | Pscan-ChIP | production service resource, data analysis service, service resource, analysis 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 | 2026-08-02 09:05:48 | 5 | |||||||
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MBGD - Microbial Genome Database Resource Report Resource Website 50+ mentions |
MBGD - Microbial Genome Database (RRID:SCR_012824) | database, data or information resource | MBGD is a database for comparative analysis of completely sequenced microbial genomes, the number of which is now growing rapidly. The aim of MBGD is to facilitate comparative genomics from various points of view such as ortholog identification, paralog clustering, motif analysis and gene order comparison. The heart of MBGD function is to create orthologous or homologous gene cluster table. For this purpose, similarities between all genes are precomputed and stored into the database, in addition to the annotations of genes such as function categories that were assigned by the original authors and motifs that were found in the translated sequence. Using these homology data, MBGD dynamically creates orthologous gene cluster table. Users can change a set of organisms or cutoff parameters to create their own orthologous grouping. Based on this cluster table, users can further analyze multiple genomes from various points of view with the functions such as global map comparison, local map comparison, multiple sequence alignment and phylogenetic tree construction. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: National Institute for Basic Biology; Okazaki; Japan |
nif-0000-03105, biotools:mbgd | https://bio.tools/mbgd | SCR_012824 | MBGD | 2026-08-02 09:06:03 | 58 | ||||||||
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CUPSAT Resource Report Resource Website 50+ mentions |
CUPSAT (RRID:SCR_010773) | CUPSAT | production service resource, data analysis service, service resource, analysis 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 | 2026-08-02 09:05:53 | 74 |
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