PEDE (Pig Expression Data Explorer) is a database of porcine EST collections derived from full-length cDNA libraries and full-length sequences of the cDNA clones picked from the EST collection. To catalog the full-length mRNA sequences expressed in pigs, we constructed oligo-capped cDNA libraries of various swine tissues; thus far, we have performed EST analyses using libraries from 15 kinds of tissues and cells. The EST sequences (190 370 at the end of August 2006; the current sequencing status can be viewed here) have been clustered and assembled (10 562 contigs and 57 276 singlets having > 50 bases at Phred QV > 20), and we have determined their similarity to sequences in RefSeq, and UniGene. We have also performed full-length cDNA determination, and, to date, we have completed sequencing of 10 147 cDNA clones; these sequences also are stored into the database with annotation according to the similarity analyses. The PEDE database system was constructed to store sequences and similarity data of our swine full-length cDNA libraries and to make them available to users. PEDE provides interfaces for keyword and ID searches of BLAST results and enables users to obtain sequence data and names of clones of interest. Putative SNPs in EST assemblies have been classified according to breed specificity and their effect on coding amino acids, and the assemblies are equipped with an SNP search interface.

The PEDE database is a valuable resource because it contains porcine nucleotide sequences and cDNA clones that are ready for analyses such as expression in mammalian cells, because of their high likelihood of containing full-length CDS. PEDE will be useful for researchers who want to explore genes that may be responsible for traits such as disease susceptibility. The database also offers information regarding major and minor porcine-specific antigens, which maight be investigated in regard to the use of pigs as models in various medical research applications.