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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GenomeTraFaC Resource Report Resource Website 1+ mentions |
GenomeTraFaC (RRID:SCR_007686) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 29,2022. Whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs | gene orthologs, human mrna, mouse mrna | PMID:17178752 | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-02902 | SCR_007686 | GenomeTraFaC | 2026-08-10 09:33:18 | 2 | ||||||||
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Genome Reviews Resource Report Resource Website 1+ mentions |
Genome Reviews (RRID:SCR_007685) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented April 24, 2017. The Genome Reviews database provides an up-to-date, standardized and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes. Currently, Genome Reviews contains the genomes of archaea, bacteria, bacteriophages and selected eukaryota. Genome Reviews is available as a MySQL relational database, or a flat file format derived from that in the EMBL Nucleotide Sequence Database. An Ensembl-style browser is now available for Genome Reviews, providing a zoomable graphical view of all chromosomes and plasmids represented in the database. The location and structure of all genes is shown and the distribution of features throughout the sequence is displayed. | complete genome sequence, genome sequence, nucleotides, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
European Union FELICS contract 021902 (RII3); European Union TEMBLOR contract QLRI- CT-2001000015 |
PMID:16901215 PMID:15608201 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02899, biotools:genomereviews | https://bio.tools/genomereviews | SCR_007685 | Genome Reviews Database | 2026-08-10 09:33:13 | 4 | |||||
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Human Organized Whole Genome Database Resource Report Resource Website |
Human Organized Whole Genome Database (RRID:SCR_007721) | HOWDY | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A database system for retrieve human genome information in different data sources that are available to public. The information you could find here is automatically extracted from the genetic databases and shown with all data having the identifiers in common and linking to one another. HOWDY facilitates obtaining information of human genes by using official symbols and aliases approved by HGNC, GDB and Entrez Gene. It also provides a graphical view of the Human Genome maps for the finished contigs as well as radiation hybrid maps. | human genome | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02981 | SCR_007721 | Human Organized Whole Genome Database | 2026-08-10 09:33:15 | 0 | ||||||||
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Computational Hot Spots of Protein Interfaces Resource Report Resource Website 1+ mentions |
Computational Hot Spots of Protein Interfaces (RRID:SCR_007720) | data or information resource, database | It provides information about the evolutionary history of the residues on the interface and represents which residues are highly conserved on the interface. In this way, functionally and structurally important residues on the interface can be distinguished. Hotsprint contains overall properties of the interface such as number of computational hot spots on the interface, number of conserved residues on the interface, average conservation score of interface residues and buried ASA of the interface. Additionally, residues of the interface along with their position, name, conservation score, ASA in monomer, ASA in complex, type (contacting interface residue, neighboring interface residue or none) and whether the residue is computational hot spot or not information are presented. | evolution of proteins, protein residues, surface residues | has parent organization: Koc University; Istanbul; Turkey | nif-0000-02980 | SCR_007720 | HotSprint | 2026-08-10 09:33:18 | 1 | |||||||||
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GenoBase Resource Report Resource Website 1+ mentions |
GenoBase (RRID:SCR_007682) | data or information resource, database | A database of high-throughput data being collected to understand comprehensively the living E. coli K-12 model cell. GenoBase is a public repository for sequence information, proteome, transcription, and metabolome data. The GenoBase contains columns labeled Gene, Synonym, ECK, Genome, ID, Left, Right, Direction, Description, Comment, and Status. The table displays two rows for each gene: one row shows data for the E. coli K-12 MG1655 genome; the other shows data for the E. coli K-12 W3110 genome. Left, Right, and direction give the coordinates and orientation of the gene. Search/Clip allows the user to find information in GenoBase based on gene, position, or DNA sequence. References is currently not fully operational. Other search allows execution of an SQL query., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | e. coli, e coli k-12 model cell, escheria coli, k-12, metabolome, proteome, transcription, model | is listed by: 3DVC | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02894 | http://sal.cs.purdue.edu:8097/GB7/index.jsp | SCR_007682 | GenoBase | 2026-08-10 09:33:13 | 8 | |||||||
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Genetics Home Reference Resource Report Resource Website 50+ mentions |
Genetics Home Reference (RRID:SCR_007681) | data or information resource, database | Genetics Home Reference provides consumer-friendly information about the effects of genetic variations on human health. Genetics Home Reference contains condition summaries (describing major features of genetic conditions), gene summaries (describing normal function, chromosomal location, etc), and gene family summaries. | gene summary, genetic condition, health, human genetics, FASEB list | nif-0000-02889 | SCR_007681 | Genetics Home Reference | 2026-08-10 09:33:14 | 63 | ||||||||||
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Genome information broker Resource Report Resource Website 1+ mentions |
Genome information broker (RRID:SCR_007684) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 28, 2013. GIB is a comprehensive data repository of complete microbial genomes in the public domain. GIB will diffuse the genome sequence data and annotation in a day whenever the data is submitted to the International Nucleotide Sequence Databases (DDBJ, EMBL database and GenBank). You can explore any microbial genome by clone name, ORF name/number, function, gene name, product name, location, sequence (namely, homology search), and other features/qualifiers defined by INSD. The result of query is displayed either in graphics or in a table format. | microbe, microbe genome sequence, microbial genome | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02897 | http://ecoliwiki.net/colipedia/index.php/Genome_Information_Broker_(GIB) | SCR_007684 | Genome Information Broker | 2026-08-10 09:33:14 | 2 | ||||||||
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HORDE - Human Olfactory Receptor Data Exploratorium Resource Report Resource Website 10+ mentions |
HORDE - Human Olfactory Receptor Data Exploratorium (RRID:SCR_007719) | data or information resource, database | HORDE (The Human Olfactory Data Explorer) is a database of human Olfactory Receptors (ORs), the largest multigene family in multicellular organisms. You will find here information on the OR proteins, their gene structure and their genomic organization. Also available are OR repertoires of other mammalian species, along with a set of analysis tools. human olfactory receptor, :OR, OR proteins, olfactory receptor, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | human olfactory receptor, human olfactory receptors, olfactory receptor, or, or proteins | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02979 | SCR_007719 | HORDE | 2026-08-10 09:33:14 | 22 | |||||||||
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Human PAML Browser Resource Report Resource Website 1+ mentions |
Human PAML Browser (RRID:SCR_007715) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It provides access to the results of tests for positive selection in 14,000 human genes. Multiple alignments of protein-coding regions of genes from human and other mammals were extracted from whole-genome alignments available from UC-Santa Cruz. Each gene was analyzed using the maximum likelihood tests of selection using PAML. Branch, site, and branch+site tests were performed, each with at least one matching null model. | positive selection, protein | has parent organization: Case Western Reserve University; Ohio; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02996 | SCR_007715 | Human PAML Browser | 2026-08-10 09:33:15 | 1 | ||||||||
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Hoppsigen Resource Report Resource Website 1+ mentions |
Hoppsigen (RRID:SCR_007718) | data or information resource, database | Hoppsigen is a nucleic database of homologous processed pseudogenes. It contains 5,823 human retroelements and 3,934 mouse retroelements. These retroelements were annotated and stored in the database HOPPSIGEN (Homologous processed pseudogenes). Sequences were grouped in families considering their homologies. The database contains 3,168 families of exclusively human (1,966) or mouse retroelements (1,202) and 323 families containing human and mouse retroelements. 5,206 human retroelements were annotated as processed pseudogenes (respectively 3,428 mouse retroelements). The database contains functional genes from ENSEMBL homologous to Hoppsigen retroelements. | human retroelements, mouse retroelements, pseudogenes | has parent organization: Claude Bernard University Lyon 1; Lyon; France | nif-0000-02978 | SCR_007718 | Hoppsigen | 2026-08-10 09:33:15 | 3 | |||||||||
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EICO DB - Expression-based Imprint Candidate Organiser Resource Report Resource Website |
EICO DB - Expression-based Imprint Candidate Organiser (RRID:SCR_007637) | data or information resource, database | EICO DB is an integrated database for discovery of novel imprinted genes. EICO DB provides candidate imprinted genes by cDNA microarray and single Nucleotide Polymorphisms between MSM and C57BL/6J within RIKEN mouse full-lenght cDNA for validation of imprinting. The tools provided by the website are candidate Imprinted Transcripts by Expression (CITE), MoUse SNP CATalog (MuSCAT), EICO DAS Server, and EICO Wiki. | cdna microarray, novel gene, novel imprinted gene, snp | nif-0000-02792 | http://fantom2.gsc.riken.jp/EICODB/ | SCR_007637 | EICO-DB | 2026-08-10 09:33:13 | 0 | |||||||||
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Encyclopedia of Hepatocellular Carcinoma Genes Online Resource Report Resource Website 1+ mentions |
Encyclopedia of Hepatocellular Carcinoma Genes Online (RRID:SCR_007636) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. ECHO is a web resource of Hepatocellular Carcinoma genes. The fundamental part of EHCO2 is the collections of thirteen gene sets related to HCC. It also contains tools to search by homology, pathway, or phenotype. | hepatocellular carcinoma, hepatocellular carcinoma gene, oncology | has parent organization: Academia Sinica; Taipei; Taiwan | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02791 | https://www.hsls.pitt.edu/obrc/index.php?page=URL1151599427 | SCR_007636 | EHCO | 2026-08-10 09:33:17 | 7 | |||||||
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Proteome Database of Lactococcus lactis Resource Report Resource Website 1+ mentions |
Proteome Database of Lactococcus lactis (RRID:SCR_007633) | data or information resource, database | It presents an advanced online database for dynamic access to proteomes and two-dimensional (2D) gels. The database was designed to administer complete in silico proteomes and links them with experimental proteomic data in the manner of 2D electrophoresis gels (IPG-Dalt). The 2D gels serve as reference maps in 2D gel analysis as well as tools for navigation of the database to switch between experimental and predicted data. Therefore, all identified spots in the gels are clickable and linked with summarized protein information. The protein information tables contain calculated characteristics, which are often used in proteomics, such as the molecular weight, isoelectric point, codon adaptation index, grand average of hydropathicity, etc. The design of the database permits online extension of gel data and protein attributes without knowledge of any software language. Besides navigation via 2D gels, the clear graphical user interface permits quick and intuitive searching throughout complete proteomes and supports, e.g. the search for proteins with isoelectric points within pH ranges of interest or protein classes (e.g. ribosomal proteins or transporters). The first organism implemented in the database is Lactococcus lactis. | nif-0000-02776 | SCR_007633 | DynaProt 2D | 2026-08-10 09:33:17 | 1 | |||||||||||
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DRC - Database of Ribosomal Crosslinks Resource Report Resource Website |
DRC - Database of Ribosomal Crosslinks (RRID:SCR_007628) | DRC | data or information resource, database | A database of published cross-link data of the E. coli ribosome. The website provides information on rRNA-rRNA cross-links, rRNA-rProteins cross-links, cross-links between ribosomal proteins, tRNA-ribosome cross-links, growing peptide-ribosome cross-links, factors-ribosome cross-links, and mRNA-ribosome cross-links. All data are presented in tables. | e coli, escheria coli, factors-ribosome cross-links, cross-links between ribosomal proteins, growing peptide-ribosome cross-links, mrna-ribosome cross-links, ribosome, rrna-rproteins cross-links, rrna-rrna cross-links, trna-ribosome cross-links | is listed by: 3DVC | nif-0000-02766 | http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/ | SCR_007628 | 2026-08-10 09:33:13 | 0 | ||||||||
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Integr8 : Access to complete genomes and proteomes Resource Report Resource Website 50+ mentions |
Integr8 : Access to complete genomes and proteomes (RRID:SCR_007740) | data or information resource, database | The Integr8 web portal provides easy access to integrated information about deciphered genomes and their corresponding proteomes. Available data includes DNA sequences (from databases including the EMBL Nucleotide Sequence Database, Genome Reviews, and Ensembl); protein sequences (from databases including the UniProt Knowledgebase and IPI); statistical genome and proteome analysis (performed using InterPro, CluSTr, and GOA); and information about orthology, paralogy, and synteny. | bio.tools |
is listed by: bio.tools is listed by: Debian is related to: InteroPorc has parent organization: European Bioinformatics Institute |
nif-0000-03027, biotools:intergr8 | https://bio.tools/intergr8 | SCR_007740 | Integr8 | 2026-08-10 09:33:15 | 52 | ||||||||
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FLAGdb++ Resource Report Resource Website 1+ mentions |
FLAGdb++ (RRID:SCR_007659) | data or information resource, database | A database for the functional analysis of the Arabidopsis genome. The ultimate objective of this project is to develop a database and associated bioinformatics tools based on the integration of genomic data around a selection of plant complete genomes. This tool will help users to understand the biological role of plant genes by considering them in a wide context: a multigene family, a topological environment, and/or a functional network. The database and the associated user-friendly interface is developed with a conceptual effort for the graphical display and the hierarchical organization of the data. The running integration involves the structural and functional international annotations, EST from different plant species, novel gene predictions, mutant tags, gene families, protein motifs, transcriptome data, repeat sequences, primers and tags for genomic approaches (DNA chips, synteny studies, BAC library screening, RT-PCR, SNP discovery, ...), subcellular targeting, secondary structures, 3D models, MPSS tags, curated annotations and mutant phenotypes. | arabidopsis, arabidopsis genome, plant genome | nif-0000-02840 | SCR_007659 | FLAGdb++ | 2026-08-10 09:33:13 | 9 | ||||||||||
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F-SNP: a collection of functional SNPs, specifically prioritized for disease association studies Resource Report Resource Website 100+ mentions |
F-SNP: a collection of functional SNPs, specifically prioritized for disease association studies (RRID:SCR_007653) | data or information resource, database | F-SNP database provides integrated information about the functional effects of SNPs obtained from 16 bioinformatics tools and databases. The functional effects are predicted and indicated at the splicing, transcriptional, translational, and post-translational level. As such, the F-SNP database helps identify and focus on SNPs with potential pathological effect to human health. Users can find SNP's based on ID, associated disease, gene, or chromosomal region. | functional snp, disease-associated snp, snp, snp functional effect, snp pathogenicity, FASEB list | has parent organization: Queens University; Ontario; Canada | nif-0000-02832 | SCR_007653 | F-SNP | 2026-08-10 09:33:17 | 131 | |||||||||
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EXProt- database for EXPerimentally verified Protein functions Resource Report Resource Website 10+ mentions |
EXProt- database for EXPerimentally verified Protein functions (RRID:SCR_007652) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. EXProt (database for EXPerimentally verified Protein functions) is a new non-redundant database containing protein sequences for which the function has been experimentally verified. EXProt is a selection of 6491 entries which are described to have an experimentally verified function. The entries in EXProt all have a unique ID number and provide information about organism, protein sequence, functional annotation, link to entry in original database, and if known, gene name and link to references in PubMed. The EXProt database can be searched with BLAST or FASTA with amino acid or nucleotide sequence as query sequence. Note that only the sequence goes into the field. EXProt database is also searchable in SRS6 at CMBI. In a near future entries from the genome project of Lactobacillus plantarum by Wageningen Centre for Food Sciences (WCFS) will be added to EXProt. | protein function, protein sequence | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02828 | SCR_007652 | EXProt | 2026-08-10 09:33:12 | 15 | |||||||||
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FireDB Resource Report Resource Website 1+ mentions |
FireDB (RRID:SCR_007655) | FireDB | data or information resource, database | A database of Protein Data Bank structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt accession numbers as well as keywords. FireDB contains information on every chemical compound in the PDB, including their descriptions, the PDB structures in which the compounds are found and the amino acids that are in contact with the ligand. | protein, protein structure, pdb, bio.tools |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is listed by: bio.tools is listed by: Debian has parent organization: Spanish National Cancer Research Center |
nif-0000-02839, biotools:firedb | https://bio.tools/firedb | SCR_007655 | 2026-08-10 09:33:12 | 7 | ||||||||
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Functional Coverage of the Proteome Resource Report Resource Website 1+ mentions |
Functional Coverage of the Proteome (RRID:SCR_007654) | data or information resource, database | FCP is a publicly accessible web tool dedicated to analyzing the current state and trends of available proteome structures along the classification schemes of enzymes and nuclear receptors. It offers both graphical and quantitative data on the degree of functional coverage in that portion of the proteome by existing structures and on the bias observed in the distribution of those structures among proteins. Users can choose to search the website based on structures or ligands, and can also sort by enzyme or receptor. Users can also view data based on structural and population (species) filters. | enzyme, nuclear receptor, protein, proteome, proteome structure | has parent organization: Pompeu Fabra University; Barcelona; Spain | nif-0000-02834 | SCR_007654 | FCP | 2026-08-10 09:33:13 | 2 |
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