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Nucleic Acids Research, 2004, Vol. 32, Database issue D484-D488
© 2004 Oxford University Press

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

Hirohide Uenishi*,1,3, Tomoko Eguchi2,3, Kohei Suzuki2,3, Tetsuya Sawazaki2,3, Daisuke Toki2,3, Hiroki Shinkai2,3, Naohiko Okumura2,3, Noriyuki Hamasima1,3 and Takashi Awata1,3

1 Genome Research Department, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba, Ibaraki 305-8602, Japan, 2 Second Research Division, STAFF-Institute and 3 Animal Genome Research Program, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0864, Japan

*To whom correspondence should be addressed at Animal Genome Laboratory, Genome Research Department, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba, Ibaraki 305-8602, Japan. Tel/Fax: +81 29 838 8627; Email: huenishi{at}affrc.go.jp
+AB116555–AB116564, BP137499–BP173623 and BP433030–BP464980

We generated the PEDE (Pig EST Data Explorer; http://pede.dna.affrc.go.jp/) database using se quences 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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