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Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04)
An IDC-based Algorithm for Efficient Homology Filtration with Guaranteed Seriate Coverage
Taichung, Taiwan, ROC
May 19-May 21
ISBN: 0-7695-2173-8
Hsiao Ping Lee, National Tsing-Hua University, Taiwan
Yin Te Tsai, Providence University, Taiwan
Ching Hua Shih, National Tsing-Hua University, Taiwan
Tzu Fang Sheu, National Tsing-Hua University, Taiwan
Chuan Yi Tang, National Tsing-Hua University, Taiwan
The homology search within genomic databases is a fundamental and crucial work for biological knowledge discovery. With exponentially increasing sizes and accesses of databases, the filtration approach, which filters impossible homology candidates to reduce the time for homology verification, becomes more important in bioinformatics. Most of known gram-based filtration approaches, like QUASAR, in the literature have limited error tolerance and would conduct potentially higher false-positives. In this paper, we present an IDC-based lossless filtration algorithm with guaranteed seriate coverage and error tolerance for efficient homology discovery. In our method, the original work of homology extraction with requested seriate coverage and error levels is transformed to a longest increasing subsequence problem with range constraints, and an efficient algorithm is proposed for the problem in this paper. The experimental results show that the method significantly outperforms QUASAR. On some comparable sensitivity levels, our homology filter would make the discovery more than three orders of magnitude faster than that QUASAR does, and more than four orders faster than the exhaustive search.
Citation:
Hsiao Ping Lee, Yin Te Tsai, Ching Hua Shih, Tzu Fang Sheu, Chuan Yi Tang, "An IDC-based Algorithm for Efficient Homology Filtration with Guaranteed Seriate Coverage," bibe, pp.395, Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04), 2004
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