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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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rSNP Guide Resource Report Resource Website 1+ mentions |
rSNP Guide (RRID:SCR_000087) | data or information resource, database | A system of databases which stores information on the influence of mutations in regulatory gene regions . This tool helps recognize protein binding sites that are being altered by mutation. It has four cross-linked sub databases that focus on specific aspects including: (1) the effect of single nucleotide mutations in regulatory gene regions and their interaction with nuclear proteins; (2) references to original publications on the subject; (3) the experimental details of these publications; and (4) the protocols of these experiments. This resource is aimed at providing information to further research on the influence of specific sequence alterations on disease susceptibility, drug resistance and healthcare. | database, single nucleotide mutations, RNA, DNA, nuclear proteins, protein binding sites, drug resistance, disease susceptibility, health care, regulatory gene regions, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Siberian Branch of the Russian Academy of Sciences; Novosibirsk; Russia |
Open Source | nif-0000-03428, biotools:rsnp_guide | https://bio.tools/rsnp_guide | SCR_000087 | rSNP Guide | 2026-02-11 10:55:59 | 1 | |||||||
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dbSTS Resource Report Resource Website 1+ mentions |
dbSTS (RRID:SCR_000400) | dbSTS | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences. | genomic, mapping, sequence, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
NIH | PMID:2781285 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:dbsts, nif-0000-20939, r3d100010649 | https://bio.tools/dbsts https://doi.org/10.17616/R39P5C |
SCR_000400 | NCBI dbSTS: database of Sequence Tagged Sites, Sequence Tagged Sites Database, NCBI dbSTS, dbSTS: database of Sequence Tagged Sites, Database of Sequence Tagged Sites | 2026-02-11 10:56:02 | 3 | ||||
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Interolog/Regulog Database Resource Report Resource Website 1+ mentions |
Interolog/Regulog Database (RRID:SCR_000755) | data or information resource, database | Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. | interacting, interolog, protein, regulog, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:15173116 | nif-0000-20863, biotools:interolog | https://bio.tools/interolog | SCR_000755 | Interolog | 2026-02-11 10:56:07 | 2 | |||||||
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ProGlycProt Resource Report Resource Website 1+ mentions |
ProGlycProt (RRID:SCR_000622) | ProGlycProt | data or information resource, database | Manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. The database is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoproteins, defined as entries with at least one experimentally known glycosylated residue (glycosite). Whereas, ProUGP is the supplementary section, presenting uncharacterized prokaryotic glycoproteins, defined as entries with experimentally identified glycosylation but unidentified glycosites. The ProGlycProt has been developed with to aid and advance the emerging scientific interests in understanding the mechanisms, implications, and novelties of protein glycosylation in prokaryotes that include many pathogenic as well as economically important bacterial species. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology. A general data update policy is once in three months. Existing entries are updated in real-time. | glycoprotein, glycosite, glycosylation, coding gene, protein, glycosylation type, attached glycan, oligosaccharyl transferase, glycosyl transferase, glycobiology, glycosylating enzyme, glycosylation linked gene, crystal structure, homology, homology model, blast, predict, bacteria, archaea, image collection, structure, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Institute of Microbial Technology; Chandigarh; India |
Institute of Microbial Technology; Chandigarh; India OLP0063; Council of Scientific and Industrial Research; New Delhi; India SIP10AA |
PMID:22039152 | nlx_151583, biotools:proglycprot | https://bio.tools/proglycprot | SCR_000622 | Prokaryotic Glycoproteins, ProGlycProt - A Repository of Experimentally Characterized GlycoProteins of Prokaryotes | 2026-02-11 10:56:05 | 1 | |||||
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AnimalTFDB Resource Report Resource Website 100+ mentions |
AnimalTFDB (RRID:SCR_001624) | AnimalTFDB | data or information resource, database | A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, dna-binding domain, transcription co-factor, chromatin remodeling factor, gene structure, functional domain, go annotation, protein interaction, ortholog, paralog, 3d structure, pathway, protein-protein interaction, binding site, target, data set, image collection, 3d spatial image, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Ensembl has parent organization: Huazhong University of Science and Technology; Wuhan; China |
Huazhong University of Science and Technology; Wuhan; China ; Fundamental Research Funds for the Central Universities 2010MS045; National Natural Science Foundation of China 31171271 |
PMID:22080564 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153892, OMICS_01856, biotools:animal_tfdb | https://bio.tools/animal_tfdb | SCR_001624 | Animal Transcription Factor Database | 2026-02-11 10:56:16 | 289 | ||||
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COSMIC - Catalogue Of Somatic Mutations In Cancer Resource Report Resource Website 1000+ mentions |
COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) | COSMIC | data or information resource, database |
Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats. Some key features of COSMIC are: * Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types. * Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines. |
cancer, mutation, somatic mutation, tumor, cancer genome, genome, gene, dna, tissue, histology, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Cancer | Wellcome Trust 077012/Z/05/Z | PMID:20952405 | Free | nif-0000-02690, biotools:cosmic, OMICS_00082 | http://www.sanger.ac.uk/perl/CGP/cosmic https://bio.tools/cosmic |
SCR_002260 | Catalogue Of Somatic Mutations In Cancer | 2026-02-11 10:56:26 | 4486 | |||
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WebGeSTer DB Resource Report Resource Website 1+ mentions |
WebGeSTer DB (RRID:SCR_002165) | WebGeSTer DB | data or information resource, database | Database of intrinsic terminators of transcription that is comprized of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. Information about structural parameters of individual terminators such as sequence, length of stem and loop, mismatches and gaps, U-trail, genomic coordinates and gene name and accession number is available in both tabular form and as a composite figure. Summary statistics for terminator profiles of whole genome can be also obtained. Raw data files for individual genomes can be downloaded (.zip files) for detailed investigations. Data is organized into different tiers such that users can fine-tune their search by entering name of the species, or taxon ID or genomes with a certain number of terminators. To visualize the occurrence of the terminators, an interactive map, with the resolution to single gene level, has been developed. | genome, terminator, transcription, plasmid, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20972211 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:webgester_db, OMICS_01862 | https://bio.tools/webgester_db | SCR_002165 | WebGesTer Database, Web Genome Scannner for Terminators Database, WebGeSTer DB - A Transcription Terminator Database | 2026-02-11 10:56:24 | 5 | |||||
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EchoBASE Resource Report Resource Website 1+ mentions |
EchoBASE (RRID:SCR_002430) | EchoBASE | data or information resource, database | A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium. | gene, bio.tools |
is listed by: bio.tools is listed by: Debian |
GlaxoSmithKline ; BBSRC |
PMID:15608209 | nif-0000-02781, biotools:echobase, r3d100011646 | https://bio.tools/echobase https://doi.org/10.17616/R38W6H |
SCR_002430 | EchoBASE: an integrated post-genomic database for Escherichia coli | 2026-02-11 10:56:32 | 6 | |||||
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DOMINE: Database of Protein Interactions Resource Report Resource Website 1+ mentions |
DOMINE: Database of Protein Interactions (RRID:SCR_002399) | DOMINE | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Database of known and predicted protein domain (domain-domain) interactions containing interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions. DOMINE contains a total of 26,219 domain-domain interactions (among 5,410 domains) out of which 6,634 are inferred from PDB entries, and 21,620 are predicted by at least one computational approach. Of the 21,620 computational predictions, 2,989 interactions are high-confidence predictions (HCPs), 2,537 interactions are medium-confidence predictions (MCPs), and the remaining 16,094 are low-confidence predictions (LCPs). (May 2014) | domain-domain interaction, prediction, protein domain, interaction, protein domain interaction, protein, domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Pfam has parent organization: University of Texas at Dallas; Texas; USA |
PMID:21113022 PMID:17913741 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01906, nif-0000-02758, biotools:domine | https://bio.tools/domine | SCR_002399 | Database of Protein Domain Interactions | 2026-02-11 10:56:28 | 1 | |||||
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PubGene Resource Report Resource Website 10+ mentions |
PubGene (RRID:SCR_002119) | data or information resource, database | It helps users retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a gene-centric database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a literature network organizing information in a form that is easy to navigate. | gene, information, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is parent organization of: Coremine Medical |
Free, Freely Available | biotools:pubgene, nif-0000-20908 | https://bio.tools/pubgene | SCR_002119 | PubGene | 2026-02-11 10:56:23 | 39 | |||||||
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DBETH - Database for Bacterial ExoToxins for Humans Resource Report Resource Website 1+ mentions |
DBETH - Database for Bacterial ExoToxins for Humans (RRID:SCR_005908) | DBETH | data or information resource, database | Database of Bacterial ExoToxins for Human is a database of sequences, structures, interaction networks and analytical results for 229 exotoxins, from 26 different human pathogenic bacterial genus. All toxins are classified into 24 different Toxin classes. The aim of DBETH is to provide a comprehensive database for human pathogenic bacterial exotoxins. DBETH also provides a platform to its users to identify potential exotoxin like sequences through Homology based as well as Non-homology based methods. In homology based approach the users can identify potential exotoxin like sequences either running BLASTp against the toxin sequences or by running HMMER against toxin domains identified by DBETH from human pathogenic bacterial exotoxins. In Non-homology based part DBETH uses a machine learning approach to identify potential exotoxins (Toxin Prediction by Support Vector Machine based approach). | sequence, structure, interaction network, human, pathogen, bacterial genus, toxin, bacteria, exotoxin, homology, homolog, structure, sequence, domain, prediction, mechanism, activity, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: CSIR - Indian Institute of Chemical Biology; Kolkata; India |
Council of Scientific and Industrial Research; New Delhi; India | PMID:22102573 | nlx_149481, biotools:dbeth | https://bio.tools/dbeth | SCR_005908 | Database for Bacterial ExoToxins for Humans | 2026-02-11 10:57:16 | 2 | |||||
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TRANSFAC Resource Report Resource Website 100+ mentions |
TRANSFAC (RRID:SCR_005620) | TRANSFAC | data or information resource, database | Manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. Used to predict potential transcription factor binding sites. | Curated, eucaryotic, transcription, factor, genomic, binding, site, sequence, regulated, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: Gene Regulation Databases is related to: TRANSPATH is related to: Babelomics is related to: GeneTrail works with: rVista |
European Commission ; German Ministry of Education and Research |
PMID:12520026 | Free, Freely available | biotools:transfac, nif-0000-03576 | http://www.biobase-international.com/pages/index.php?id=transfac http://gene-regulation.com/pub/databases.html https://bio.tools/transfac |
SCR_005620 | 2026-02-11 10:57:08 | 261 | |||||
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IndelFR - Indel Flanking Region Database Resource Report Resource Website 1+ mentions |
IndelFR - Indel Flanking Region Database (RRID:SCR_006050) | IndelFR | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Indel Flanking Region Database is an online resource for indels and the flanking regions of proteins in SCOP superfamilies, including amino acid sequences, lengths, locations, secondary structure constitutions, hydrophilicity / hydrophobicity, domain information, 3D structures and so on. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid insertion/deletions(indels), substitutions and the relationship between them. The indels were obtained through the pairwise alignment of homologous structures in SCOP superfamilies. The IndelFR database contains 2,925,017 indels with flanking regions extracted from 373,402 structural alignment pairs of 12,573 non-redundant domains from 1053 superfamilies. IndelFR has already been used for molecular evolution studies and may help to promote future functional studies of indels and their flanking regions. | indel, flanking region, protein, structural domain, domain, protein superfamily, protein structure, insertion/deletion, insertion, deletion, protein sequence, sequence, structure, protein domain, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: SCOP: Structural Classification of Proteins is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Shandong University; Shandong; China |
Independent Innovation Foundation of Shandong University 2009JC006; National Natural Science Foundation of China 30970092; National Natural Science Foundation of China 61070017; Scientific Research Reward Fund for excellent Young and Middle-Aged scientists in Shandong Province 20090451326 |
PMID:22127860 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:indelfr, nlx_151448 | https://bio.tools/indelfr | SCR_006050 | IndelFR: Indel Flanking Region Database, Indel Flanking Region Database | 2026-02-11 10:57:18 | 2 | ||||
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SNPedia Resource Report Resource Website 50+ mentions |
SNPedia (RRID:SCR_006125) | SNPedia | data or information resource, database | Wiki investigating human genetics including information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA. It is based on a wiki model in order to foster communication about genetic variation and to allow interested community members to help it evolve to become ever more relevant. As the cost of genotyping (and especially of fully determining your own genomic sequence) continues to drop, we''''ll all want to know more - a lot more - about the meaning of these DNA variations and SNPedia will be here to help. SNPedia has been launched to help realize the potential of the Human Genome Project to connect to our daily lives and well-being. For more information see the Wikipedia page, http://en.wikipedia.org/wiki/SNPedia * Download URL: http://www.SNPedia.com/index.php/Bulk * Web Service URL: http://bots.SNPedia.com/api.php | dna, genetics, gene, genome, genoset, genotype, medicine, medical condition, genetic variation, dna, genetic variation, genomics, single nucleotide polymorphism, medical association, phenotypic association, genealogical association, variation, genome annotation, phenotype, web service, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:22140107 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 | biotools:snpedia, grid.465250.0, nlx_151604 | https://ror.org/0253rdk33 https://bio.tools/snpedia |
SCR_006125 | 2026-02-11 10:57:20 | 62 | ||||||
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RNA CoSSMos Resource Report Resource Website 1+ mentions |
RNA CoSSMos (RRID:SCR_006120) | RNA CoSSMos | data or information resource, database | Database to search through the nucleic acid structures from the Protein Data Bank and examine structural motifs, including (a)symmetric internal loops, bulge loops, and hairpin loops. They have compiled over 2,000 three-dimensional structures, which can now be searched using different parameters, including PDB information, experimental technique, sequence, and motif type. RNA secondary structure is important for designing therapeutics, understanding protein-RNA binding and predicting tertiary structure of RNA. Several databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. To create the RNA CoSSMos database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop''''s structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the database. False positives were defined, identified and reclassified or omitted from the database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos database is updated weekly. | secondary structure motif, rna, three-dimensional structure, internal loop, bulge loop, hairpin loop, motif, nucleic acid, structure, secondary structure, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Saint Louis University; Missouri; USA |
NIGMS 1R15GM085699-01A1 | PMID:22127861 | Freely accessible, Acknowledgement requested | nlx_151597, biotools:rna_cossmos | https://bio.tools/rna_cossmos | SCR_006120 | Znosko Lab RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database, Znosko Lab CoSSMos Database, RNA Characterization of Secondary Structure Motifs (RNA CoSSMos), RNA CoSSMos Database, RNA CoSSMos - Characterization of Secondary Structure Motifs, RNA Characterization of Secondary Structure Motifs | 2026-02-11 10:57:14 | 1 | ||||
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NRG-CING Resource Report Resource Website 1+ mentions |
NRG-CING (RRID:SCR_006079) | NRG-CING | data or information resource, database | NRG-CING presents a complete validation report for all 9,000+ wwPDB NMR entries including remediated experimental data such as chemical shifts from BMRB and restraints from NRG . These CING reports are compiled from internal analyses and those by CCPN, DSSP, PROCHECK-NMR/Aqua, ShiftX, Talos+, Vasco, Wattos, and WHAT_CHECK. The NRG-CING website is a collection of CING reports that has been pre-calculated for all PDB files solved by NMR. (See website for more information on CING.) In case the underlying experimental data is available, these have been cleaned up and made syntactically and semantically correct and homogeneous. For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists used in the structure calculation are accessible, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. Assessment of the quality of the structural result is paramount to their usage and a combined, integrated repository of both input data and structural results greatly facilitates such an analysis. In addition, the accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculations using the available experimental data and present-day software with improved protocols and force fields. Such efforts, however, generally fail on over half of all deposited structures due to the syntactic and semantic heterogeneity of the data and the wide variety of formats used for their deposition. We have combined the cleaned-up restraints information from the NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank in the weekly updated NRG-CING database. Eleven programs, in addition to CING itself, have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available restraint and chemical shift data. The longitudinal validation of this data yielded a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The cleaned up NMR experimental datasets and the validation reports are freely available. | macromolecular structure, nmr, macromolecule, restraint, chemical shift, validation report, validation, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Worldwide Protein Data Bank (wwPDB) is related to: NMR Restraints Grid is related to: Biological Magnetic Resonance Data Bank (BMRB) has parent organization: Radboud University; Nijmegen; The Netherlands |
Netherlands Organization for Scientific Research (NWO) 700.55.443; Netherlands Bioinformatics Centre (NBIC) ; EU FP6 LSHG-CT-2005-018988; EU FP6 LHSG-CT-2004-512092; EU FP7 261572; Brussels Institute for Research and Innovation BB2B 2010-1-12; NLM LM05799 |
PMID:22139937 | Free | nlx_151486, biotools:nrg-cing | https://bio.tools/nrg-cing | SCR_006079 | 2026-02-11 10:57:19 | 1 | |||||
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ProPortal Resource Report Resource Website 1+ mentions |
ProPortal (RRID:SCR_006112) | ProPortal | data or information resource, database | ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization--from the genome to the ecosystem--embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococcus strains, 11 Synechococcus strains and 28 cyanophage strains that infect one or both groups. Cyanobacterial and cyanophage genes are clustered into orthologous groups that can be accessed by keyword search or through a genome browser. Users can also identify orthologous gene clusters shared by cyanobacterial and cyanophage genomes. Gene expression data for Prochlorococcus ecotypes MED4 and MIT9313 allow users to identify genes that are up or downregulated in response to environmental stressors. In addition, the transcriptome in synchronized cells grown on a 24-h light-dark cycle reveals the choreography of gene expression in cells in a ''natural'' state. Metagenomic sequences from the Global Ocean Survey from Prochlorococcus, Synechococcus and phage genomes are archived so users can examine the differences between populations from diverse habitats. Finally, an example of cyanobacterial population data from the field is included. | genomic, metagenomic, transcriptomic, field data, marine cyanobacterium, genome, ecosystem, ecotypic variation, microbial taxon, phage, genome, gene, orthologous gene cluster, cyanobacteria, cyanophage genome, population dynamics, microarray, metagenome, protein, cyanophage, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
NSF OCE-0425602; NSF EF0424599; DOE DE-FG02-02ER63445; DOE DE-FG02-08ER64516; DOE DE-FG02-07ER64506; Gordon and Betty Moore Foundation award letter 495.01 |
PMID:22102570 | Public | nlx_151586, biotools:proportal | https://bio.tools/proportal | SCR_006112 | Prochlorococcus Portal | 2026-02-11 10:57:14 | 9 | ||||
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Dr.VIS - Human Disease-Related Viral Integration Sites Resource Report Resource Website 1+ mentions |
Dr.VIS - Human Disease-Related Viral Integration Sites (RRID:SCR_005965) | Dr.VIS, Dr. VIS | data or information resource, database | Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromosome, cytoband, gene and refseq position as specific as possible. Viral-cellular junction sequences are extracted from papers and nucleotide databases, and linked to corresponding integration sites Graphic views summarizing distribution of viral integration sites are generated according to chromosome maps. Dr.VIS is built with a hope to facilitate research of human diseases and viruses. Dr.VIS provides curated knowledge of integration sites from chromosome region narrow to genomic position, as well as junction sequences if available. Dr.VIS is an open resource for free. | disease, virus, viral integration, viral integration site, integration site, malignant disease, chromosome region, genomic position, viral-host junction sequence, junction sequence, oncogene, chromosome, catalog, graphic interface, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Tongji University; Shanghai; China |
State Key Basic Research Program 973 2011CB910204; National Natural Science Foundation of China ; Major State Basic Research Development Program ; 863 Hi-Tech Program of China ; National Key Technology R&D Program in the 11th Five Year Plan of China ; Major State Basic Research Development Program of China |
PMID:22135288 | Open - Free to browse and download data in Dr.VIS. | nlx_151323, biotools:dr.vis | http://www.scbit.org/dbmi/drvis https://bio.tools/dr.vis |
SCR_005965 | Dr. VIS - Database of Human Disease-related Viral Integration Sites, Database of Human Disease-related Viral Integration Sites | 2026-02-11 10:57:12 | 1 | ||||
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FunTree Resource Report Resource Website 1+ mentions |
FunTree (RRID:SCR_006014) | FunTree | data or information resource, database | FunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH. To access the resource enter a specific CATH superfamily code or search for a structure / sequence / function (either via a EC code or KEGG ligand / reaction ID, PDB ID or UniProtKB ID). Or browse the resource via superfamily / function / structure / metabolites & reactions via the menu on the left panel. FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme''''s sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering 1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms. | enzyme function, enzyme superfamily, enzyme, sequence, structure, phylogenetic, chemical, mechanistic, functional annotation, superfamily, gold standard, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CATH: Protein Structure Classification is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: KEGG is related to: UniProtKB has parent organization: European Bioinformatics Institute |
European Molecular Biology Laboratory; Heidelberg; Germany ; BBSRC ; Wellcome Trust 081989/Z/07/A; DOE contract DE-AC02-06CH11357 |
PMID:22006843 | Free | biotools:funtree, nlx_151402 | https://bio.tools/funtree | SCR_006014 | 2026-02-11 10:57:13 | 4 | |||||
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VirusMINT Resource Report Resource Website 10+ mentions |
VirusMINT (RRID:SCR_005987) | VirusMINT | data or information resource, database | A virus protein interactions database that collects and annotates all the interactions between human and viral proteins and integrates this information in the human protein interaction network. It uses the PSI-MI standard and is fully integrated with the MINT database. You can search for any viral or human protein by entering either common names or database identifiers or display a complete viral interactome. | protein interaction, virus, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: PSI-MI is related to: VirHostNet: Virus-Host Network is related to: MINT has parent organization: University of Rome Tor Vergata; Rome; Italy |
Papilloma virus, Human immunodeficiency virus, Epstein-Barr virus, Hepatitis B virus, Hepatitis C virus, Herpes virus, Simian virus 40 | PMID:18974184 | nif-0000-03636, OMICS_01909, biotools:virusmint, r3d100010685 | https://bio.tools/virusmint https://doi.org/10.17616/R3F890 |
SCR_005987 | 2026-02-11 10:57:12 | 16 |
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