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Please use this identifier to cite or link to this item: http://ntour.ntou.edu.tw:8080/ir/handle/987654321/27815

Title: Length Encoded Secondary Structure Profile for Remote Homologous Protein Detection
Authors: Yen-Chu Hsu;Chien-Ming Chen;Tun-Wen Pai;Jyh-Fu Jeng;Chin-Hua Hu;Wen-Shyong Tzou
Contributors: NTOU:Department of Computer Science and Engineering
國立臺灣海洋大學:資訊工程學系
Keywords: protein sequence comparison;secondary structure element alignment;dynamic programming;length encoded profile;protein folding
Date: 2009
Issue Date: 2011-10-21T02:34:06Z
Publisher: the 9th International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP 2009)
Abstract: Abstract:Protein data has an explosive increasing rate both in volume and diversity, yet many of its structures remain unresolved, as well their functions remain to be identified. The conventional sequence alignment tools are insufficient in remote homology detection, while the current structural alignment tools would encounter the difficulties for proteins of unresolved structure. Here, we aimed to overcome the combination of two major obstacles for detecting remote homologous proteins: proteins with unresolved structure, and proteins of low sequence identity but high structural similarity. We proposed a novel method for improving the performance of protein matching problem, especially for mining remote homologous proteins. In this study, existing secondary structure prediction techniques were applied to provide the locations of secondary structure elements of proteins. The proposed LESS (Length Encoded Secondary Structure) profile was then constructed for segment-based similarity comparison in parallel computing. As compared to a conventional residue-based sequence alignment tool, detection of remote protein homologies through LESS profile is favourable in terms of speed and high sequence diversity, and its accuracy and performance can improve the deficiencies of the traditional primary sequence alignment methodology. This method may further support biologists in protein folding, evolution, and function prediction.
Relation: LNCS 5574, pp.1-11
URI: http://ntour.ntou.edu.tw/handle/987654321/27815
Appears in Collections:[資訊工程學系] 演講及研討會

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