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Title: Ordered combinatorial feature selection: An information portal for multiple indexing sequence alignment
Authors: Hsin-Wei Wang;Jian-Ming Chen;Wei-Yao Chou;Margaret Dah-Tsyr Chang;Tun-Wen Pai
Contributors: NTOU:Department of Computer Science and Engineering
Keywords: combinatorial feature;exclusive group feature;multiple indexing sequence alignment;protein family
Date: 2007-05
Issue Date: 2011-10-21T02:34:18Z
Publisher: International Symposium on Bioinformatics Research and Applications
Abstract: Abstract:An ordered combinatorial feature database is designed for identification of sequential consensus motifs as important functional and/or structurally critical peptides for all protein families defined by Pfam. The ordered combinatorial features in the proposed database are extracted from each protein family employing a multiple indexing sequence alignment that performs interval jumping searching algorithms and center-star alignments. The interval jumping searching algorithm is designed to find consensus motifs by using the combination of hashing encoding, quick sorting and interval jumping techniques, which provides an alternative manner to achieve approximate matching functions in linear time. The center-star alignment identifies combinatorial features among the query sequences, and the hierarchical clustering algorithms combining with bitwise comparison operations perform exclusive group feature extraction for each individual subgroup. In this research, all protein families defined by the Pfam database are pre-analyzed by the proposed algorithm, and their respective combinatorial group features are collected in a database for further referencing and applications. To verify the biological meanings of the searched patterns, each feature was scanned by Prosite (release 20.4), and a hit rate of more than 73.6% was achieved for frequently occurring signatures.
Relation: pp.72-76
Appears in Collections:[Department of Computer Science and Engineering] Lecture & Seminar

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