Snat: a SNP annotation tool for bovine by integrating various sources of genomic information

BMC Genetics

Software

Li Jiang¹  Weixuan Fu¹  Jicai Jiang¹  Jian-Feng Liu¹  Bin Zhou¹  Qin Zhang¹ 

[1] Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, P.R. China;

关键词: Gene Ontology;    Genome Wide Association Study;    KEGG Pathway;    Significant SNPs;    Recent Genome Wide Association Study;   

DOI  :  10.1186/1471-2156-12-85

 received in 2011-04-15, accepted in 2011-10-07,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundMost recently, with maturing of bovine genome sequencing and high throughput SNP genotyping technologies, a large number of significant SNPs associated with economic important traits can be identified by genome-wide association studies (GWAS). To further determine true association findings in GWAS, the common strategy is to sift out most promising SNPs for follow-up replication studies. Hence it is crucial to explore the functional significance of the candidate SNPs in order to screen and select the potential functional ones. To systematically prioritize these statistically significant SNPs and facilitate follow-up replication studies, we developed a bovine SNP annotation tool (Snat) based on a web interface.ResultsWith Snat, various sources of genomic information are integrated and retrieved from several leading online databases, including SNP information from dbSNP, gene information from Entrez Gene, protein features from UniProt, linkage information from AnimalQTLdb, conserved elements from UCSC Genome Browser Database and gene functions from Gene Ontology (GO), KEGG PATHWAY and Online Mendelian Inheritance in Animals (OMIA). Snat provides two different applications, including a CGI-based web utility and a command-line version, to access the integrated database, target any single nucleotide loci of interest and perform multi-level functional annotations. For further validation of the practical significance of our study, SNPs involved in two commercial bovine SNP chips, i.e., the Affymetrix Bovine 10K chip array and the Illumina 50K chip array, have been annotated by Snat, and the corresponding outputs can be directly downloaded from Snat website. Furthermore, a real dataset involving 20 identified SNPs associated with milk yield in our recent GWAS was employed to demonstrate the practical significance of Snat.ConclusionsTo our best knowledge, Snat is one of first tools focusing on SNP annotation for livestock. Snat confers researchers with a convenient and powerful platform to aid functional analyses and accurate evaluation on genes/variants related to SNPs, and facilitates follow-up replication studies in the post-GWAS era.

【 授权许可】

Unknown   
© Jiang et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.