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http://nematode.net/

The home page of the parasitic nematode EST project at Washington University's Genome Sequencing Center, St. Louis. It was established in 2000 as a component of the NIH-NIAID grant "A Genomic Approach to Parasites from the Phylum Nematoda."

Proper citation: Nematode.net (RRID:SCR_007816) Copy   

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http://img.jgi.doe.gov/

Datasets and tools for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context. Plasmids that are not part of a specific microbial genome sequencing project and phage genomes are also included in order to increase its genomic context for comparative analysis. The user interface (see User Interface Map) allows navigating the microbial genome data space along its three key dimensions (genes, genomes, and functions), and groups together the main comparative analysis tools. Microbial genome data analysis in IMG usually starts with the definition of an analysis context in terms of selected genomes, functional annotations, and/or genes, followed by the individual or comparative analysis of genomes, functional annotations, or genes.

Proper citation: IMG (RRID:SCR_007733) Copy   

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http://www.shigen.nig.ac.jp/rice/oryzabase/

A comprehensive rice science database established in 2000 by rice researcher''s committee in Japan. The database is originally aimed to gather as much knowledge as possible ranging from classical rice genetics to recent genomics and from fundamental information to hot topics. The Oryzabase consists of five parts, (1) genetic resource stock information, (2) gene dictionary, (3) chromosome maps, (4) mutant images, and (5) fundamental knowledge of rice science. We are planning to do more extensive cross-referencing of Oryzabase to the major DNA sequence database, literature database and other plant databases in order to provide the wealth of information to rice researchers. We are calling for additional mutants and mapped gene information to incorporate into the Oryzabase. Newly identified mutants and mapped trait genes published in the scientific journals will be welcome to integrate into the Oryzabase maps.

Proper citation: Oryzabase (RRID:SCR_007840) Copy   

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http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi

OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. OrthoMCL starts with reciprocal best hits within each genome as putative in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as putative ortholog pairs. Related proteins are interlinked in a similarity graph. Then MCL (Markov Clustering algorithm,Van Dongen 2000; www.micans.org/mcl) is invoked to split mega-clusters. This process is analogous to the manual review in COG construction. MCL clustering is based on weights between each pair of proteins, so to correct for differences in evolutionary distance the weights are normalized before running MCL.

Proper citation: OrthoMCL DB: Ortholog Groups of Protein Sequences (RRID:SCR_007839) Copy   

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http://www.interfil.org

The Human Intermediate Filament Database is a continuously updated review of the intermediate filament field. It is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants. Suggestions on ways to improve the database are also welcome. The entire database can be searched through the Browse and Search options. A number of different parameters can be used to search the database including unique identifier, intermediate filament, disease DNA variations, amino acid variations, domain, date accepted, author and abstract. Output from the search is returned in a table containing all the pertinent cross referenced information. Multiple sequence alignment can also be performed via the CLUSTALW program to determine cDNA or protein sequence conservation. The database is linked to multiple other resources including NCBI RefSeq, PDB, OMIM, UCSC genome browser, NCBI Gene, HomoloGene, PubMed and HGNC. In the case of HGNC, reciprocal links are also available from HGNC that links to Human Intermediate Filament Database. Due to the protein centric nature of the Human Intermediate Filament Database and the gene centric nature of HGNC, a HGNC record will potentially link to multiple records in this database due to the presence of alternative splicing. In such an event, the Human Intermediate Filament Database will present to the user a list of all the protein records resulting from the HGNC gene record. The database uses Jalview and Jmol applets for the visualization of multiple sequence alignment and structure respectively. The database contains information on disease phenotypes of a variety of different intermediate filament related diseases.

Proper citation: Human Intermediate Filament Database (RRID:SCR_007744) Copy   

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http://www.interferome.org

Interferome is a database that provides identification of interferon regulated gene signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It will also assist in identifying regulatory elements and enable comparison of tissue expression of IRGs in human and mouse. Availability of sequence information from more than 37 species, together with comprehensive annotation will enable comparative genomics and phylogenetic analysis to be performed on these IRGs. Within the database, Type I, II and III IFN regulated genes have been manually curated from more than 28 publicly available microarray datasets. Interferon Regulated Genes (IRGs) were identified from multiple microarray and proteomic experiments where cells were treated with IFNs. Genes that were up or down regulated more than 1.5 fold relative to control samples were defined as IRGs.

Proper citation: Interferome (RRID:SCR_007743) Copy   

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http://metacyc.org/

MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1,200 pathways from more than 1,600 different organisms, and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes.

Proper citation: MetaCyc (RRID:SCR_007778) Copy   

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http://merops.sanger.ac.uk/

An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these have indexes. Each of the Summary pages offers links to supplementary pages. About 3000 individual peptidases and inhibitors are included in the database, and there is a Summary page describing each one. You can navigate to this by any of several routes. There are indexes of Name, MEROPS Identifier and source Organism on the menu bar. Each Summary page describes the classification and nomenclature of the peptidase or inhibitor, and provides links to supplementary pages showing sequence identifiers, the structure if known, literature references and more.

Proper citation: MEROPS (RRID:SCR_007777) Copy   

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http://locate.imb.uq.edu.au/

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set. The membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing peer-reviewed publications.

Proper citation: LOCATE: subcellular localization database (RRID:SCR_007763) Copy   

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http://snp500cancer.nci.nih.gov

It provides a central resource for sequence verification of SNPs. The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer. The site allows users to search for SNPs using SNP identifier, gene symbol, gene alias, chromosome location, or gene ontology pathway.

Proper citation: SNP500Cancer (RRID:SCR_007943) Copy   

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http://snap.genomics.org.cn

A sequence analysis tool providing a simple but detailed analysis of human genes and their variations. For each gene, a gene-gene relationship network can be generated based on protein-protein interaction data, metabolic pathway connections and extended through phylogenetic relations. Snap provides tools for designing sequence primers and evaluating RNA splicing effects of single SNPs - known from the databases or defined by you. Primers can be designed for the amplification or sequencing of cDNA, genomic DNA, introns only or exons only., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SNAP (RRID:SCR_007936) Copy   

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http://phylomedb.bioinfo.cipf.es

Database for phylomes, that is, complete collections of phylogenetic trees for all proteins encoded in a given genome. It aims at providing a repository of high-quality phylogenies and alignments for proteins encoded in model species. To derive a phylome, each protein encoded in a given genome is used as a seed to retrieve its homologs in other complete genomes. These sequences are aligned and processed to derive reliable phylogenies using several phylogenetic methods. Besides providing the evolutionary history of the gene families, phylomeDB includes phylogeny based predictions of orthology and paralogy relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PhylomeDB (RRID:SCR_007850) Copy   

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http://www.panzea.org

It contains the genotype, phenotype, and polymorphism data produced by the NSF-funded project; Genetic Architecture of Maize and Teosinte. The PANZEA project will identify genes that control domestication traits and three key agronomic traits: flowering time, plant height, and kernel quality. Genetic linkage, association, and fine mapping analyses will be performed on the largest and most diverse set of mapping families publicly available for any species. A large series of isogenic lines will be used to characterize allelic series and epistatic interactions. The genetic architecture of each of the four trait groups will be compared and contrasted, and the influence of recombination and past domestication bottlenecks on the genomic distribution of functional diversity will be examined. Finally, the ability of genetic architecture-based models to predict phenotype will be evaluated in a broad range of germplasm, including elite US hybrids. This project will take a step toward the ultimate goal of predicting phenotype from genotype.

Proper citation: PANZEA (RRID:SCR_007846) Copy   

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http://tdrtargets.org/

This database functions both as a website where researchers can look for information on their targets of interest; and as a tool for prioritization of targets in whole genomes. Using the database as a tool, researchers can quickly prioritize a genome of interest by performing any number of individual queries on a species of interest, then assigning numerical weights to each query (in the history page) to finally obtain a ranked list of genes by combining the weighted queries. This site is part of a WHO/TDR project seeking to exploit the availability of diverse datasets to facilitate the identification and prioritization of drug targets in pathogens causing neglected diseases.

Proper citation: TDR Targets Database (RRID:SCR_007963) Copy   

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http://ppdb.tc.cornell.edu/

A Plant Proteome DataBase for Arabidopsis thaliana and maize (Zea mays). The PPDB stores experimental data from in-house proteome and mass spectrometry analysis, curated information about protein function, protein properties and subcellular localization. Importantly, proteins are particularly curated for possible (intra) plastid location and their plastid function. Protein accessions identified in published Arabidopsis (and other Brassicacea) proteomics papers are cross-referenced to rapidly determine previous experimental identification by mass spectrometry. All protein-encoding gene models in the Arabidopsis nuclear and organellar genomes, as assembled by TAIR, as well as all maize EST assemblies (ZmGI) as assembled by DFCI Maize Gene Index project. These are all uploaded in PPDB and are linked to each other via a BLAST alignment. Thus every predicted protein in both species can be searched for experimental and other information (even if not experimentally identified).

Proper citation: PPDB: Plant Proteomics Database (RRID:SCR_007872) Copy   

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http://www.poxvirus.org

A database of information on pox viruses. Goals of this project are to acquire and annotate data on poxviruses, and to develop and utilize new tools to facilitate the study of this group of organisms. This basic research is being undertaken with an eye toward the development of novel antiviral therapies, vaccines against human orthopoxvirus infections, new approaches for the environmental detection of virions, and methods to accomplish more rapid diagnosis of disease.

Proper citation: Poxvirus Bioinformatics Resource Center (RRID:SCR_007870) Copy   

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http://www.bindingdb.org

Web accessible database of data extracted from scientific literature, focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in Protein Data Bank . Website supports query types including searches by chemical structure, substructure and similarity, protein sequence, ligand and protein names, affinity ranges and molecular weight . Data sets generated by BindingDB queries can be downloaded in form of annotated SDfiles for further analysis, or used as basis for virtual screening of compound database uploaded by user. Data are linked to structural data in PDB via PDB IDs and chemical and sequence searches, and to literature in PubMed via PubMed IDs .

Proper citation: BindingDB (RRID:SCR_000390) Copy   

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http://phospho.elm.eu.org/

Database of experimentally verified phosphorylation sites in eukaryotic proteins. Entries are manually curated with links to literature references, information about structure, interaction partners and sub-cellular compartment tissues, and sequences from the UniProt database.

Proper citation: Phospho.ELM (RRID:SCR_001109) Copy   

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http://amphibiaweb.org/

Database of information on amphibian declines, natural history, conservation, and taxonomic information for every recognized species of amphibian in the world. Species accounts are being added regularly by specialists and volunteers and they contain species descriptions, life history information, conservation status, literature references, photos and range maps for many species. Some species have complete accounts; others as yet have only photographs or distributions. But all species can be queried for taxonomic, distributional and exact specimen data. AmphibiaWeb offers a powerful mapping tool by combining museum specimen data (via HerpNET) with expert opinion range maps (from Global Amphibian Assessment/IUCN) and overlaying these onto larger maps, allowing visualization in political, satellite, hybrid, or terrain map format. AmphibiaWeb currently (Aug 13, 2013) contains 7,160 species. They have 2,966 species accounts for 2,363 species, 6,517 literature references, 558 sound files, 109 video files, and 28,218 photos of 3,887 different amphibian species. These data come from numerous individuals--see acknowledgements. They have the ambitious goal of establishing a home page for every species of amphibian in the world. In order to accomplish this goal they encourage volunteers and specialists to help prepare species accounts. If you have special interest in a particular species, please contact them.

Proper citation: AmphibiaWeb (RRID:SCR_001612) Copy   

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http://metazoa.ensembl.org/index.html

Ensembl Genomes project produces genome databases for important species from across taxonomic range, using Ensembl software system. Five sites are now available, one of which is Ensembl Metazoa, which houses metazoan species.

Proper citation: Ensembl Metazoa (RRID:SCR_000800) Copy   

•   Source: SciCrunch Registry