Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds

I-Hsuan Yang; Pao-Hsian Huang; Liang Ye; Sheng-Ho Wang; Yang-Ho Chen; Xiaoqiu Huang; Kun-Mao Chao

doi:10.1109/BIBE.2004.1317372

B
BIBE
2004
Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04)
Abstract - Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds

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Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04)

Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds

Taichung, Taiwan, ROC

May 19-May 21

ISBN: 0-7695-2173-8

	ASCII Text	x
	I-Hsuan Yang, Sheng-Ho Wang, Yang-Ho Chen, Pao-Hsian Huang, Liang Ye, Xiaoqiu Huang, Kun-Mao Chao, "Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds," 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE), pp. 411, Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04), 2004.

	BibTex	x
	@article{ 10.1109/BIBE.2004.1317372, author = {I-Hsuan Yang and Sheng-Ho Wang and Yang-Ho Chen and Pao-Hsian Huang and Liang Ye and Xiaoqiu Huang and Kun-Mao Chao}, title = {Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds}, journal ={2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)}, volume = {0}, year = {2004}, isbn = {0-7695-2173-8}, pages = {411}, doi = {http://doi.ieeecomputersociety.org/10.1109/BIBE.2004.1317372}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }

	RefWorks Procite/RefMan/Endnote	x
	TY - CONF JO - 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) TI - Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds SN - 0-7695-2173-8 SP EP A1 - I-Hsuan Yang, A1 - Sheng-Ho Wang, A1 - Yang-Ho Chen, A1 - Pao-Hsian Huang, A1 - Liang Ye, A1 - Xiaoqiu Huang, A1 - Kun-Mao Chao, PY - 2004 KW - Sequence Alignment; Database Search VL - 0 JA - 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) ER -

I-Hsuan Yang, National Taiwan University

Sheng-Ho Wang, National Taiwan University

Yang-Ho Chen, National Taiwan University

Pao-Hsian Huang, National Taiwan University

Liang Ye, Iowa State University

Xiaoqiu Huang, Iowa State University

Kun-Mao Chao, National Taiwan University

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/BIBE.2004.1317372

Biologists highly rely on good algorithms for finding homologous regions in bimolecular sequences. An advanced homology search program named PatternHunter has recently been developed. Unlike the well-known program BLAST using a consecutive model, it utilizes a spaced seed model to attain higher sensitivity. We have developed a new program, which extends PatternHunter from a single spaced model to a multiple spaced model. In this paper, we describe methods for finding optimal single and multiple spaced models.

Index Terms:

Sequence Alignment; Database Search

Citation:

I-Hsuan Yang, Sheng-Ho Wang, Yang-Ho Chen, Pao-Hsian Huang, Liang Ye, Xiaoqiu Huang, Kun-Mao Chao, "Efficient Methods for Generating Optimal Single and Multiple Spaced Seeds," bibe, pp.411, Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04), 2004

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