Data mining: concepts and techniques
Data mining: concepts and techniques
GeneFisher-Software Support for the Detection of Postulated Genes
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology
Degenerate primer selection algorithms
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
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This paper describes a new strategy for designingdegenerate primers for a given multiple alignment ofamino acid sequences. Degenerate primers are useful foramplifying homologous genes. However,when a largecollection of sequences is considered, no consensusregion may exist in the multiple alignment, making itimpossible to design a single pair of primers for thecollection. In such cases, manual methods are used to findsmaller groups from the input collection so that primerscan be designed for individual groups. Our strategyproposes an automatic grouping of the input sequences byusing clustering techniques. Conserved regions are thendetected for each individual group.Conserved regionsare scored using a BlockSimilarity score, a novelalignment scoring scheme that is appropriate for thisapplication.Degenerate primers are then designed byreverse translating the conserved amino acid sequencesto the corresponding nucleotide sequences. Our program,DePiCt, was written in BioPerl and was tested on theToll-Interleukin Receptor (TIR)and the non-TIR family ofplant resistance genes. Existing programs for degenerateprimer design were unable to find primers for these datasets.