A DNA index structure using frequency and position information of genetic alphabet

Authors:
Woo-Cheol Kim;Sanghyun Park;Jung-Im Won;Sang-Wook Kim;Jee-Hee Yoon
Affiliations:
Department of Computer Science, Yonsei University, Korea;Department of Computer Science, Yonsei University, Korea;Department of Computer Science, Yonsei University, Korea;College of Information and Communications, Hanyang University, Korea;Division of Information Engineering and Telecommunications, Hallym University, Korea
Venue:
PAKDD'05 Proceedings of the 9th Pacific-Asia conference on Advances in Knowledge Discovery and Data Mining
Year:
2005

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Abstract

Exact match queries, wildcard match queries, and k-mismatch queries are widely used in lots of molecular biology applications including the searching of ESTs (Expressed Sequence Tag) and DNA transcription factors. In this paper, we suggest an efficient indexing and processing mechanism for such queries. Our indexing method places a sliding window at every possible location of a DNA sequence and extracts its signature by considering the occurrence frequency of each nucleotide. It then stores a set of signatures using a multi-dimensional index, such as the R*-tree. Also, by assigning a weight to each position of a window, it prevents signatures from being concentrated around a few spots in indexing space. Our query processing method converts a query sequence into a multi-dimensional rectangle and searches the index for the signatures overlapped with the rectangle.