The Pig Genome Database (PiGenome): an integrated database for pig genome research

Abstract

We established the Pig Genome Database (PiGenome) for pig genome research. The PiGenome integrates and analyzes all publicly available genome-wide data on pigs, including UniGenes, sequence tagged sites (STS) markers, quantitative trait loci (QTLs) data, and bacterial artificial chromosome (BAC) contigs. In addition, we produced 69,545 expressed sequence tags (ESTs) from the full-length enriched cDNA libraries of six tissues and 182 BAC contig sequences, which are also included in the database. QTLs, genetic markers, and BAC end-sequencing information were collected from public databases. The full-length enriched EST data were clustered and assembled into unique sequences, contigs, and singletons. The PiGenome provides functional annotation, identification of transcripts, mapping of coding sequences, and SNP information. It also provides an advanced search interface, a disease browser, alternative-splicing events, and a comparative gene map of the pig. A graphical map view and genome browser can map ESTs, contigs, BAC contigs (from the National Institute of Animal Science), Sino-Danish Pig Genome Project transcripts, and UniGene onto pig genome sequences which include our 182 BAC contigs and publically available BAC sequences of the Wellcome Trust Sanger Institute. The PiGenome is accessible at http://pigenome.nabc.go.kr/ .

A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing

“…This is in contrast to the report in human and yeast where exon-skipping is the most prevalent mechanism [13,14], and it is also different from rice in which intron retention is the primary alternative splicing type [25]. The percentage of alternative 5' or 3' splicing in total alternative splicing events in this study were higher than that reported in Lim et al (2009) [49] where 8.0% of alternative 5' splicing and 3% of alternative 3' splicing were observed. We discovered that more than 18.0% of the detected genes were alternatively spliced.…”

Single nucleotide polymorphism association study for backfat and intramuscular fat content in the region between SW2098 and SW1881 on pig chromosome 61

“…In total, 5,086,700 trace files of SSC whole-genome shotgun sequences (WGS) were downloaded from TraceArchive (NCBI) in May 2008. In total, 1,188,485 UniGene EST from the porcine NCBI UniGene repository and 71,100 SUSFLECK EST sequences, which were produced from full-length enriched cDNA hbraries at the National Institute of Animal Science, RDA (Lee et al, 2009;Lim et al, 2009), were obtained. The WGS and SUSFLECK trace data were base-called using phred (P < 0.01), and only sequences of high quality were selected using the seq-Clean program (length >200) after trimming cloning vector sequences with cross-match.…”

Cytochrome P450 Pig Liver Pie: Determination of Individual Cytochrome P450 Isoform Contents in Microsomes from Two Pig Livers Using Liquid Chromatography in Conjunction with Mass Spectrometry

“…BLAST searches of identified peptides were performed against the first draft of the pig genome/proteome, PiGenome (Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea) (Lim et al, 2009).…”