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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | ||||||
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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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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 | 2026-08-06 09:27:59 | 486 | |||||||
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CleanEx Resource Report Resource Website 10+ mentions |
CleanEx (RRID:SCR_012911) | database, data or information resource | CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons. To achieve this goal, each single gene expression experiment is regularly mapped on a permanent target identifier consisting of a physical description of the targeted RNA. There is one entry per gene. To have a complete view of the transcript and its product, we also link each entry to the corresponding protein. We further provide the genomic position of the transcription start site from EPD, when available. Otherwise we give the annotated start site position in Ensembl. | gene expression, data comparison, heterogeneous expression, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SIB Swiss Institute of Bioinformatics |
nif-0000-02667, biotools:cleanex | https://bio.tools/cleanex | SCR_012911 | CleanEx | 2026-08-06 09:28:04 | 28 | ||||||||
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MINAS - Metal Ions in Nucleic AcidS Resource Report Resource Website 1+ mentions |
MINAS - Metal Ions in Nucleic AcidS (RRID:SCR_013145) | MINAS | database, data or information resource | Database compiling the detailed information on innersphere, outersphere and larger coordination environment of >70,000 metal ions of 36 elements found in >2000 structures of nucleic acids contained today in the PDB and NDB. MINAS is updated monthly with new structures and offers a multitude of search functions, e.g. the kind of metal ion, metal-ligand distance, innersphere and outersphere ligands defined by element or functional group, residue, experimental method, as well as PDB entry-related information. The results of each search can be saved individually for later use with so-called miniPDB files containing the respective metal ion together with the coordination environment within a 15 A radius. MINAS thus offers a unique way to explore the coordination geometries and ligands of metal ions together with the respective binding pockets in nucleic acids. | metal ion, binding pocket, nucleic acid, metal-ligand distance, innersphere ligand, outersphere ligand, ligand, element, functional group, residue, protein databank, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: Nucleic Acid Database is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Zurich; Zurich; Switzerland |
Swiss National Science Foundation PP002-68733/1 | PMID:22096233 | nlx_151459, biotools:minas | https://bio.tools/minas | SCR_013145 | Metal Ions in Nucleic AcidS, MINAS - A Database of Metal Ions in Nucleic AcidS | 2026-08-06 09:28:04 | 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 | 2026-08-06 09:28:00 | 58 | ||||||||
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Mouse Genome Database Resource Report Resource Website 500+ mentions |
Mouse Genome Database (RRID:SCR_012953) | MGD | database, data or information resource | Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. | gene, genome, genetic, chromosome, clone, cytogenetic, dna, genomic, inbred, mammalian, mouse, mutant, ortholog, phenotype, primer, protein, reagent, sequence, strain, bio.tools |
is used by: DisGeNET is listed by: Debian is listed by: bio.tools is related to: Mouse Genome Informatics (MGI) has parent organization: Jackson Laboratory |
NHGRI HG000330 | PMID:21051359 | biotools:mgi, biotools:mgd, nif-0000-10301 | http://www.informatics.jax.org/mgihome/projects/overview.shtml, https://bio.tools/mgd, https://bio.tools/mgi | SCR_012953 | Mouse Genome Informatics: Mouse Genome Database, MGID, Mouse Genome Informatics Database | 2026-08-06 09:28:04 | 502 | |||||
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SYFPEITHI: A Database for MHC Ligands and Peptide Motifs Resource Report Resource Website 100+ mentions |
SYFPEITHI: A Database for MHC Ligands and Peptide Motifs (RRID:SCR_013182) | SYFPEITHI | database, data or information resource | SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. It contains a collection of MHC class I and class II ligands and peptide motifs of humans and other species, such as apes, cattle, chicken, and mouse, for example, and is continuously updated. Searches for MHC alleles, MHC motifs, natural ligands, T-cell epitopes, source proteins/organisms and references are possible. Hyperlinks to the EMBL and PubMed databases are included. In addition, ligand predictions are available for a number of MHC allelic products. The database is based on previous publications on T-cell epitopes and MHC ligands. It contains information on: -Peptide sequences -anchor positions -MHC specificity -source proteins, source organisms -publication references Since the number of motifs continuously increases, it was necessary to set up a database which facilitates the search for peptides and allows the prediction of T-cell epitopes. The prediction is based on published motifs (pool sequencing, natural ligands) and takes into consideration the amino acids in the anchor and auxiliary anchor positions, as well as other frequent amino acids. The score is calculated according to the following rules: The amino acids of a certain peptide are given a specific value depending on whether they are anchor, auxiliary anchor or preferred residue. Ideal anchors will be given 10 points, unusual anchors 6-8 points, auxiliary anchors 4-6 and preferred residues 1-4 points. Amino acids that are regarded as having a negative effect on the binding ability are given values between -1 and -3. Sponsors: SYFPEITHI is supported by DFG-Sonderforschungsbereich 685 and theEuropean Union: EU BIOMED CT95-1627, BIOTECH CT95-0263, and EU QLQ-CT-1999-00713. | epitope, allele, allelic, amino acid, ape, bind, cattle, chicken, class i, class ii, human, immunological database, ligand, mhc, molecule, motif, mouse, natural, organism, peptide, product, protein, sequence, specie, t-cell, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Tubingen; Tubingen; Germany |
nif-0000-21383, biotools:syfpeithi | https://bio.tools/syfpeithi | SCR_013182 | SYFPEITHI | 2026-08-06 09:28:06 | 258 | |||||||
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psRNATarget Resource Report Resource Website 1000+ mentions |
psRNATarget (RRID:SCR_013321) | psRNATarget | data analysis service, production service resource, analysis service resource, service resource | A plant small RNA target analysis server which features two important analysis functions: 1) reverse complementary matching between miRNA and target transcript using a proven scoring schema, and 2) target site accessibility evaluation by calculating unpaired energy (UPE) required to ?open? secondary structure around miRNA?s target site on mRNA. PsRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of miRNA/target site pairs that may affect miRNA binding activity to target transcript. PsRNATarget is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded miRNAs and transcript sequences; and outputs a comprehensive list of miRNA / target pairs along with the online tools for batch downloading, key word searching and results sorting., 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:21622958 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00414, biotools:psrnatarget | https://bio.tools/psrnatarget | SCR_013321 | psRNATarget: A Plant Small RNA Target Analysis Server | 2026-08-06 09:28:06 | 1040 | |||||
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ApiDB CryptoDB Resource Report Resource Website 10+ mentions |
ApiDB CryptoDB (RRID:SCR_013455) | ApiDB CryptoDB | database, data or information resource | An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data | cryptosporidium parvum, cryptosporidium, cryptosporidium genome, cryptosporidium orf, cryptosporidium sage tag alignments, cryptosporidium snp, genomic sequence, dna motif, snp, est, orf, data set, bio.tools |
uses: SynView is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Eukaryotic Pathogen Database Resources |
NIAID contract HHSN266200400037C | PMID:16381902 | nif-0000-02698, biotools:cryptodb, r3d100012265 | https://bio.tools/cryptodb | http://cryptodb.org/ | SCR_013455 | CryptoDB, Cryptosporidium Genomics Resource | 2026-08-06 09:28:08 | 25 | ||||
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GENSCAN Resource Report Resource Website 500+ mentions |
GENSCAN (RRID:SCR_013362) | genscan | data analysis service, production service resource, analysis service resource, service resource | Web server for identification of complete gene structures in genomic DNA.Tool for predicting locations and exon-intron structures of genes in genomic sequences from variety of organisms. Used for prediction of complete gene structures in human genomic DNA. | complete gene structures identyfication, genomic DNA, predicting locations, exon-intron structures, genomic sequences, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Stanford University; Stanford; California has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
PMID:9149143 | Restricted | biotools:genscan, OMICS_01494 | https://bio.tools/genscan | SCR_013362 | GENSCAN Web Server at MIT | 2026-08-06 09:28:07 | 765 | |||||
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eProbalign Resource Report Resource Website |
eProbalign (RRID:SCR_013247) | data analysis service, production service resource, analysis service resource, service resource | Data analysis service that computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. | multiple sequence alignments, partition function posterior probabilities, bio.tools |
uses: Probalign is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: New Jersey Institute of Technology; New Jersey; USA |
NIGMS R01 GM073082 | PMID:17485479 | OMICS_00975, biotools:eprobalign | https://bio.tools/eprobalign | SCR_013247 | eProbalign web server, EProbalign | 2026-08-06 09:28:06 | 0 | ||||||
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Cube-DB Resource Report Resource Website 1+ mentions |
Cube-DB (RRID:SCR_013233) | Cube-DB | database, data or information resource | Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orhtologous protein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described on documentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera). | protein, functional divergence, vertebrate, genome, ortholog, protein sequence, data set, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Bioinformatics Institute; Singapore; Singapore |
PMID:22139934 | nlx_149432, biotools:cube-db | https://bio.tools/cube-db | SCR_013233 | Cube-DB: Detection of Functional Divergence in Human Protein Families | 2026-08-06 09:28:05 | 3 | ||||||
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UniCarbKB Resource Report Resource Website 10+ mentions |
UniCarbKB (RRID:SCR_014410) | database, data or information resource | International effort which has created a glycomics knowledgebase with access to a database of information on the glycan structures of glycoproteins. It serves as and promotes an online information storage and search platform for glycomics and glycobiology research. Open access knowledgebase offers resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental and functional data. | knowledgebase, glycomics, glycerin structure, glycoprotein, cell line, glycoproteomics knowledge platform, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Macquarie University; Sydney; Australia has parent organization: University of Gothenburg; Gothenburg; Sweden has parent organization: SIB Swiss Institute of Bioinformatics is parent organization of: UniCarb-DB |
DOI:10.1093/nar/gkt1128 | Free, Freely available | biotools:unicarbkb | https://bio.tools/unicarbkb | http://www.unicarbkb.org | SCR_014410 | 2026-08-06 09:28:20 | 27 | ||||||
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ExPASy ABCD database Resource Report Resource Website 10+ mentions |
ExPASy ABCD database (RRID:SCR_017401) | ABCD ExPASy, The ABCD database | database, data or information resource | Repository of sequenced antibodies, integrating curated information about antibody and its antigen with cross links to standardized databases of chemical and protein entities. Manually curated repository of sequenced antibodies, developed by Geneva Antibody Facility at University of Geneva, in collaboration with CALIPHO and Swiss Prot groups at SIB Swiss Institute of Bioinformatics. Database provides list of sequenced antibodies with their known targets. Each antibody is assigned unique ID number that can be used in academic publications to increase reproducibility of experiments. | Sequenced antibody, manually curated, known target, ExPASy, repository, chemically defined antibodies, antibody, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal is related to: SIB Swiss Institute of Bioinformatics has parent organization: University of Geneva; Geneva; Switzerland |
University of Geneva ; ProCare Foundation ; Swiss National Science Foundation |
PMID:31410491 | Free, Freely available | SCR_019000, biotools:AbCD_database | https://bio.tools/ABCD_database | SCR_017401 | ExPASy ABCD (AntiBodies Chemically Defined) Database, The ABCD database, AntiBodies Chemically Defined, AntiBodies Chemically Defined Expert Protein Analysis System database, ExPASy ABCD Database, The AntiBodies Chemically Defined Database | 2026-08-06 09:29:04 | 10 | ||||
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SnpSift Resource Report Resource Website 500+ mentions |
SnpSift (RRID:SCR_015624) | source code, software toolkit, software resource | Software toolkit for filtering and manipulating annotated files. After annotation, the software's filter function can find relevant genomic variants in large data files. | annotation, filtering, genomic variant, single nucleotide polymorphism, bio.tools |
is listed by: bio.tools is listed by: Debian works with: SnpEff |
PMID:22728672 | Open Source, Free, Available for download | biotools:snpsift | https://bio.tools/snpsift | SCR_015624 | SnpEff | 2026-08-06 09:28:40 | 591 | ||||||
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Open Trials Resource Report Resource Website 1+ mentions |
Open Trials (RRID:SCR_015570) | database, data or information resource | Database that contains data such as registry entries, portions of regulatory documents describing individual trials, structured data on methods and results, and researchers and papers from and/or related to clinical trials. The initiative aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally. | clinical trial, clinical trial database, clinical trial data, open database, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Oxford; Oxford; United Kingdom |
Laura and John Arnold Foundation ; Wellcome Trust ; World Health Organisation ; West of England Academic Health Science Network |
Open source | biotools:opentrials | https://bio.tools/opentrials | SCR_015570 | 2026-08-06 09:28:40 | 3 | |||||||
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Genome Aggregation Database Resource Report Resource Website 1000+ mentions |
Genome Aggregation Database (RRID:SCR_014964) | gnomAD | database, data or information resource | Database that aggregates exome and genome sequencing data from large-scale sequencing projects. The gnomAD data set contains individuals sequenced using multiple exome capture methods and sequencing chemistries. Raw data from the projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects. | database, genome, , bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: Broad Institute Genomics Platform has parent organization: Broad Institute has parent organization: Broad Institute of MIT and Harvard |
Broad Institute | Open source, Available to the biomedical community, The community can contribute to this resource | biotools:gnomad | https://github.com/macarthur-lab/gnomad_browser/issues, https://bio.tools/gnomad | SCR_014964 | gnomAD 2.0, gnomAD Browser, gnomAD version 2.0, Exome Aggregation Consortium | 2026-08-06 09:28:29 | 4229 |
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