Tissue related in-silico mining of single nucleotide polymorphisms (SNPS) from expressed sequence tags (ESTS) in livestock species

Abstract

Tissue specific Single nucleotide polymorphisms (SNPs) hold significance as potential expressed Quantitative Trait Loci (eQTL). Although there have been numerous studies for mining SNPs in livestock species, there is little focus on discovery of tissue-specific SNPs.  We performed tissue related in-silico SNP mining from Expressed Sequence Tags (ESTs) in two livestock species - pig and cattle. EST data for tissues such as skin, liver, spleen, intestine and mammary gland for the two species were downloaded from NCBI website.  ESTs were pre-processed using the online tool EGassembler and assembled into contigs using CAP3 program.  SNPs were predicted from contigs using Quality SNP tool. Contigs were searched in the genome assembly of a species using Blat tool in UCSC genome browser.  Perl scripts were written to find genomic position of SNPs from the alignment of contigs with the genomic segments, and to find availability of predicted SNPs in the dbSNP database. A database of tissue related SNPs was developed.