In silico detection of single nucleotide polymorphisms in expressed sequence tags of European sea bass
Souche, E.; Hellemans, B.; Canario, A.; Klages, S.; Reinhardt, R.; Volckaert, F.A.M.J. (2007). In silico detection of single nucleotide polymorphisms in expressed sequence tags of European sea bass, in: Mees, J. et al. (Ed.) VLIZ Young Scientists' Day, Brugge, Belgium 2 March 2007: book of abstracts. VLIZ Special Publication, 39: pp. 57
In: Mees, J.; Seys, J. (Ed.) (2007). VLIZ Young Scientists' Day, Brugge, Belgium 2 March 2007: book of abstracts. VLIZ Special Publication, 39. Vlaams Instituut voor de Zee (VLIZ): Oostende. IX, 82 pp.
In: VLIZ Special Publication. Vlaams Instituut voor de Zee (VLIZ): Oostende. ISSN 1377-0950
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. Around 30,000 European sea bass (Dicentrarchus labrax) Expressed Sequence Tags (ESTs) have been sequenced and processed at the Max Planck Institute for Molecular Genetics. Since 55.1% (16,117) ESTs are redundant, they provide a resource for in silico SNP discovery. To prevent the detection of sequencing errors, a redundancy of 2 is required for a mismatch to be considered a candidate SNP (Picoult- Newberg et al., 1999). Thus, only contigs containing more than 4 overlapping sequences are analysed. 974 (21.3%) contigs qualify for in silico SNPs discovery, representing 5,548 (19%) ESTs and 478,232 base pairs. Various tools are used to detect candidate SNPs; so far, 2 software packages have been tried. 246 candidate SNPs, of which 56 indels, were proposed by SNPServer using default parameters (Savage et al., 2005). Less stringent parameters lead to the discovery of 1027 candidate SNPs, of which 267 indels. PolyBayes (Marth et al., 1999) selected 772 candidates SNPs, of which 231 indels. The Primer3 software is used to design primers flanking each candidate SNP, which are validated in the laboratory by sequencing. Polymorphisms will be mapped, used for selection in aquaculture and the study of adaptation in natural populations.
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