Lim Dajeong, Cho Yong-Min, Lee Kyung-Tai, Kang Yeonkyung, Sung Samsun, Nam Jungrye, Park Eung-Woo, Oh Sung-Jong, Im Seok-Ki, Kim Heebal
Department of Agricultural Biotechnology, Seoul National University (SNU), Seoul, 151-742, South Korea.
Mamm Genome. 2009 Jan;20(1):60-6. doi: 10.1007/s00335-008-9156-3. Epub 2008 Dec 10.
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/ .
我们建立了用于猪基因组研究的猪基因组数据库（PiGenome）。PiGenome整合并分析了所有公开可用的猪全基因组数据，包括单基因（UniGenes）、序列标签位点（STS）标记、数量性状基因座（QTLs）数据以及细菌人工染色体（BAC）重叠群。此外，我们从六个组织的全长富集cDNA文库中产生了69,545个表达序列标签（ESTs）以及182个BAC重叠群序列，这些也都包含在数据库中。QTLs、遗传标记和BAC末端测序信息是从公共数据库收集的。全长富集EST数据经过聚类并组装成独特序列、重叠群和单拷贝序列。PiGenome提供功能注释、转录本鉴定、编码序列定位以及SNP信息。它还提供了一个高级搜索界面、一个疾病浏览器、可变剪接事件以及猪的比较基因图谱。图形图谱视图和基因组浏览器可以将ESTs、重叠群、BAC重叠群（来自韩国国立动物科学研究所）、中丹猪基因组计划转录本以及单基因定位到猪基因组序列上，这些猪基因组序列包括我们的182个BAC重叠群以及威康信托桑格研究所公开可用的BAC序列。可通过http://pigenome.nabc.go.kr/访问PiGenome。
