Description Description PEDE (Pig EST Data Explorer) is a database of porcine EST collections derived from full-length cDNA libraries. 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 analysis using libraries from thymus, spleen, peripheral blood mononuclear cells, uterus, ovary, liver, and lung. The EST sequences (83 564 at the end of May 2003; the current sequencing status can be viewed here) have been clustered and assembled (5546 contigs and 28 461 singlets having > 50 bases at Phred QV > 20), and we have determined their similarity to sequences registered in public databases, RefSeq, and UniGene. 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 have been classified according to breed specificity and their effect on coding amino acids, and the assemblies of ESTs 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 should be investigated in the use of pigs for medical applications.