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.
This work was supported by the Korea Research Foundation Grant (KRF-2004-003-D00302), the Basic Research Program Grant (Grant R04-2003-000-10048-0), and the IT Research Center via Cheju National University.
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Kim, WC., Park, S., Won, JI., Kim, SW., Yoon, JH. (2005). A DNA Index Structure Using Frequency and Position Information of Genetic Alphabet. In: Ho, T.B., Cheung, D., Liu, H. (eds) Advances in Knowledge Discovery and Data Mining. PAKDD 2005. Lecture Notes in Computer Science(), vol 3518. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11430919_21
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DOI: https://doi.org/10.1007/11430919_21
Publisher Name: Springer, Berlin, Heidelberg
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