Identification of 1,531 cSNPs from Full-length Enriched cDNA Libraries of the Korean Native Pig Using in Silico Analysis.

Oh,  Younshin; Nguyen,  Dinh Truong; Park,  Kwangha; Dirisala,  Vijaya R; Choi,  Hojun; Park,  Chankyu

doi:2009.7.2.65

Genomics Inform > Volume 7(2); 2009 > Article

Original Article

Genomics & Informatics 2009;7(2): 65-84.

DOI: https://doi.org/10.5808/gi.2009.7.2.065

Identification of 1,531 cSNPs from Full-length Enriched cDNA Libraries of the Korean Native Pig Using in Silico Analysis.

Younshin Oh, Dinh Truong Nguyen, Kwangha Park, Vijaya R Dirisala, Hojun Choi, Chankyu Park

Department of Animal Biotechnology, Konkuk University, Seoul 143-701, Korea. chankyu@konkuk.ac.kr

Abstract

Sequences from the clones of full-length enriched cDNA libraries serve as valuable resources for functional genomics related studies, genome annotation and SNP discovery. We analyzed 7,392 high-quality chromatograms (Phred value >30) obtained from sequencing the 5' ends of clones derived from full-length enriched cDNA libraries of Korean native pigs including brainstem, liver, cerebellum, neocortex and spleen libraries. In addition, 50,000 EST sequence trace files obtained from GenBank were combined with our sequences to identify cSNPs in silico. The process generated 11,324 contigs, of which 2,895 contigs contained at least one SNP and among them 610 contigs had a minimum of one sequence from Korean native pigs. Of 610 contigs, we randomly selected 262 contigs and performed in silico analysis for the identification of cSNPs. From the results, we identified 1,531 putative coding single nucleotide polymorphisms (cSNPs) and the SNP detection frequency was one SNP per 465 bp. A large-scale sequencing result of clones from full-length enriched cDNA libraries and identified cSNPs will serve as a useful resource to functional genomics related projects such as a pig HapMap project in the near future

Keywords: cSNP; full-length cDNA library; functional genomics; Korean native pigs; pigs