PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries | Zendy

Hirohide Uenishi | Zendy

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PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries

Author(s) -

Hirohide Uenishi

Publication year - 2003

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkh037

Subject(s) - biology , expressed sequence tag , contig , complementary dna , cdna library , database , unigene , computational biology , genetics , microbiology and biotechnology , genome , gene , computer science

We generated the PEDE (Pig EST Data Explorer; http://pede.dna.affrc.go.jp/) database using sequences assembled from porcine 5' ESTs from oligo-capped full-length cDNA libraries. Thus far we have performed EST analysis of various organs (thymus, spleen, uterus, lung, liver, ovary and peripheral blood mononuclear cells) and assembled 68,076 high-quality sequences into 5546 contigs and 28,461 singlets. PEDE provides a search interface for getting results of homology searches and enables users to obtain information on sequence data and cDNA clones of interest. Single-nucleotide polymorphisms detected through comparison of the EST sequences are classified by origin (western and oriental breeds) and are searchable in the database. This database system can accelerate analyses of livestock traits and yields information that can lead to new applications in pigs as model systems for medical research.

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