Mining for Single Nucleotide Polymorphisms in Expressed Sequence Tags

As a multitude of sequence data are published, discovering polymorphisms bioinformatically becomes a valid option. In silico Single Nucleotide Polymorphism (SNP) detection is based on the analysis of multiple alignments. Each column of an alignment is considered a slice containing one base of every sequence aligned. If a mismatch is detected, the slice is further analysed and the mismatch may be reported as a candidate SNP. About 30,000 Expressed Sequence Tags (ESTs) of the fish European sea bass have been sequenced and processed. Since ESTs are redundant, they provide a resource for in silico SNP discovery. To prevent the detection of sequencing errors, a redundancy of two is chosen in order for a mismatch to be considered a candidate SNP. Among the various tools available to detect candidate SNPs, three software packages were tested: SNPServer, PolyBayes and PolyFreq. Candidate SNPs were validated in the laboratory by cloning and sequencing. From preliminary results PolyFreq outperf...

• Type: Journal
• Year: 2007
• Where: JIB
• Authors: E. L. Souche, B. Hellemans, J. K. J. Van Houdt, A. Canario, S. Klages, R. Reinhardt, F. A. M. Volckaert
• Keywords: Candidate Snps, JIB 2007, Silico Single Nucleotide, Silico Snp Discovery