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http://www-alis.tokyo.jst.go.jp/HOWDY/

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.

Proper citation: Human Organized Whole Genome Database (RRID:SCR_007721) Copy   

•   Source: SciCrunch Registry

http://prism.ccbb.ku.edu.tr/hotsprint/

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.

Proper citation: Computational Hot Spots of Protein Interfaces (RRID:SCR_007720) Copy   

•   Source: SciCrunch Registry

http://ecoli.naist.jp/GB8/

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.

Proper citation: GenoBase (RRID:SCR_007682) Copy   

•   Source: SciCrunch Registry

http://ghr.nlm.nih.gov/

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.

Proper citation: Genetics Home Reference (RRID:SCR_007681) Copy   

•   Source: SciCrunch Registry

http://gib.genes.nig.ac.jp

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.

Proper citation: Genome information broker (RRID:SCR_007684) Copy   

•   Source: SciCrunch Registry

http://bioportal.weizmann.ac.il/HORDE/

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.

Proper citation: HORDE - Human Olfactory Receptor Data Exploratorium (RRID:SCR_007719) Copy   

•   Source: SciCrunch Registry

http://mendel.gene.cwru.edu/adamslab/cgi-bin/paml/pbrowser.py

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.

Proper citation: Human PAML Browser (RRID:SCR_007715) Copy   

•   Source: SciCrunch Registry

http://pbil.univ-lyon1.fr/databases/hoppsigen.html

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.

Proper citation: Hoppsigen (RRID:SCR_007718) Copy   

•   Source: SciCrunch Registry

https://database.riken.jp/sw/en/Expression-based_Imprint_Candidate_Organiser_DB__EICO_DB_/crib151s2rib151s45i/

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.

Proper citation: EICO DB - Expression-based Imprint Candidate Organiser (RRID:SCR_007637) Copy   

•   Source: SciCrunch Registry

http://ehco.iis.sinica.edu.tw

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.

Proper citation: Encyclopedia of Hepatocellular Carcinoma Genes Online (RRID:SCR_007636) Copy   

•   Source: SciCrunch Registry

http://www.wzw.tum.de/proteomik/lactis/

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.

Proper citation: Proteome Database of Lactococcus lactis (RRID:SCR_007633) Copy   

•   Source: SciCrunch Registry

http://owww.molgen.mpg.de/~ag_ribo/ag_brimacombe/drc/

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.

Proper citation: DRC - Database of Ribosomal Crosslinks (RRID:SCR_007628) Copy   

•   Source: SciCrunch Registry

http://defensins.bii.a-star.edu.sg/

The defensins knowledgebase is a manually curated database and information source devoted to the defensin family of antimicrobial peptides. The current version of the database holds a comprehensive collection of 363 defensin records each containing sequence, structure and activity information. A web-based interface provides access to the information and allows for text-based searching on the data fields. With the rapidly increasing interest in defensins, we hope that the knowledgebase will prove to be a valuable resource in the field of antimicrobial peptide research.

Proper citation: Defensins Knowledgebase (RRID:SCR_007623) Copy   

•   Source: SciCrunch Registry

http://dbtgr.hgc.jp/

DBTGR provides information on tunicate gene regulation, such as the location of expression, or the identified regulatory elements present in promoter sequences. The database also contains the promoters of homologous genes in multiple species to allow identification of conserved cis elements.

Proper citation: DataBase of Tunicate Gene Regulation (RRID:SCR_007620) Copy   

•   Source: SciCrunch Registry

http://apps.sanbi.ac.za/ddoc/

:DDOC provides a comprehensive compilation of the published research related to the genes associated with ovarian cancer. DDOC provides details of the cell line, tissue or cell type, expression status, disease stage, tumor grade, OC type and laboratory method provided in the literature. The links to the relevant sources of data used to extract information related to genes are also included. Many aspects of the information provided in the DDOC were curated by biologists, which increases its accuracy. DDOC is freely accessible for academic and non-profit users.

Proper citation: Dragon Database for Exploration of Ovarian Cancer Genes (RRID:SCR_007621) Copy   

•   Source: SciCrunch Registry

http://dbptm.mbc.nctu.edu.tw/

dbPTM is a database that compiles information on protein post-translational modifications (PTM) such as the modified sites, solvent accessibility of surrounding amino acids, protein secondary and tertiary structures, protein domains, and protein variations. The version 2.0 of dbPTM integrates the experimentally validated PTM sites with referable literatures from Swiss-Prot, Phospho.ELM, O-GLYCBASE, and UbiProt. In all of the collected PTM information, about 25 types of PTM with enough experimentally validated sites are trained the profile hidden Markov models (HMMs) to detect the potential PTM sites with 100% specificity against Swiss-Prot proteins. To help users investigating more detail in each type of PTM, the substrate peptide specificity such as positional amino acid frequency, solvent accessibility and secondary structure surrounding the modified sites are also provided. Moreover, the information of orthologous protein clusters is provided to users for analyzing whether the PTM sites located in the evolutionary conserved regions or not., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: dbPTM: An informational repository of proteins and post-translational modifications (RRID:SCR_007619) Copy   

•   Source: SciCrunch Registry

http://urgv.evry.inra.fr/projects/FLAGdb++/HTML/index.shtml

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.

Proper citation: FLAGdb++ (RRID:SCR_007659) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.queensu.ca/F-SNP/

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.

Proper citation: F-SNP: a collection of functional SNPs, specifically prioritized for disease association studies (RRID:SCR_007653) Copy   

•   Source: SciCrunch Registry

http://www.cmbi.kun.nl/EXProt/

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.

Proper citation: EXProt- database for EXPerimentally verified Protein functions (RRID:SCR_007652) Copy   

•   Source: SciCrunch Registry

http://firedb.bioinfo.cnio.es/

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.

Proper citation: FireDB (RRID:SCR_007655) Copy   

•   Source: SciCrunch Registry