These sites guide you to the protein databases available for proteomics and some of the bioinformatics software available for accessing these databases.

Protein and Gene Databases

Each year the journal Nucleic Acids Research (NAR) publishes an issue devoted to the databases of genes and proteins. Databases of special note are SWISS-PROT, IPI, PIR and NCBI. UniProt is “the world’s most comprehensive catalog of information about proteins”. The Bioinformatic Harvester combines the protein and gene information from 15 databases.

Proteomic and Genomic Web Services

Nucleic Acids Research also publishes an issue on web servers listing web tools that you can use such as BLAST, ESLpred, SDPpred, iMolTalk, ProMoST, and many, many others.

Peptide Atlas

Peptide atlas is a collection of MS/MS data that has been analyzed for peptide identification. The Open Proteomics Database, the Sashimi data repository, and Quartz also have proteomics mass spec data. The Global Proteome Machine (GPM) organization has a database for storing the results of searches by X!Tandem. The World 2D PAGE site lists 2D gels for many tissue samples.

Protein mods - RESID

RESID provides a comprehensive collection of the types of modifications possible for proteins. UniMod, Delta Mass are other lists of post translational modifications. FindMod is a tool for searching for modifications.

Human Proteomics Initiative

This site's goal is to annotate all the known human proteins. This annotation will include function, domain structure, subcellular location, post-translational modifications, variants, and similarities to other proteins.

Human Genome Variation Society

This site is your guide to databases that deal with mutations, polymorphisms, alleles, and SNPs. Some of these databases are oriented to specific human disorders. The Alternative Splicing Gallery shows how each gene is assembled into multiple proteins by splice variants.

ELM - Functional sites

ELM predicts functional sites in eukaryotic proteins. This site has links to dozens of other sites that examine protein motifs and domains.

The Codon Usage Database tells the codon frequency in hundreds of species.

Match Miner

MatchMiner is a set of tools that enables the user to translate between disparate ids for the same gene. It uses data from the UCSC, LocusLink, Unigene, OMIM, Affymetrix and Jackson data sources to determine how different ids relate. Supported id types include, gene symbols and names, IMAGE and FISH clones, GenBank accession numbers and UniGene cluster ids.