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JIB
2007

Mining for Single Nucleotide Polymorphisms in Expressed Sequence Tags

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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...
E. L. Souche, B. Hellemans, J. K. J. Van Houdt, A.
Added 15 Dec 2010
Updated 15 Dec 2010
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
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