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Title: Oligonucleotide Selection for Molecular Taxa Classification via Microarray Technology Using Special Types of Multiple Sequence Alignments
P172
von Rohr, Peter (1); Roth, Alexander (1); Frey, Jürgen (2)

vonrohr@inf.ethz.ch
(1)Institute of Scientific Computing, Swiss Federal Institute of Technology Zurich (ETHZ),(2)Swiss Federal Research Station of Horticulture and Viticulture Waedenswil

This poster reports initial results of an ongoing research project in the area of molecular taxa classification. We are aiming at classifying a wide variety of taxa using customly built oligonucleotide microarrays. An algorithm to select oligonucleotides from genomic sequence data is proposed. This algorithm is based on multiple sequence alignments. The type of multiple sequence alignment that is chosen by the algorithm depends on the type of sequence data that we want to use for the classification system.
Currently we are focusing on coding region of the cytochrome oxidase I (COI) gene as well as on simulated sequence data. We are aligning the DNA regions of interest for a variety of taxa for which genomic DNA sequence data is available. The alignment is based on the protein sequences of the respective coding DNA regions, using the DNA sequence as additional information for gap placement. The regions for potential oligonucleotides useful for taxa classification can then be chosen based on site-specific alignment scores derived from PAM scoring matrices. The most interesting regions with regards to oligonucleotides are the regions with minimum site-specific alignment scores.