PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries.
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.
Uenishi
Hirohide
H
Genome Research Department, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba, Ibaraki 305-8602, Japan. huenishi@affrc.go.jp
Eguchi
Tomoko
T
Suzuki
Kohei
K
Sawazaki
Tetsuya
T
Toki
Daisuke
D
Shinkai
Hiroki
H
Okumura
Naohiko
N
Hamasima
Noriyuki
N
Awata
Takashi
T
D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D018076:DNA, Complementary / Q000235:genetics*; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D015723:Gene Library; D023281:Genomics; D016247:Information Storage and Retrieval; D020407:Internet; D008969:Molecular Sequence Data; D009928:Organ Specificity; D013552:Swine / Q000235:genetics*; D014584:User-Computer Interface
D018076:DNA, Complementary