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題名 Length Encoded Secondary Structure Profile for Remote Homologous Protein Detection
作者 鄭至甫
Jeng, Jyh‐Fu
貢獻者 科管智財所
關鍵詞 protein sequence comparison;secondary structure element alignment;dynamic programming;length encoded profile;protein folding
日期 2009
上傳時間 7-Nov-2014 16:02:31 (UTC+8)
摘要 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.
關聯 Lecture Notes in Computer Science, 5574, 1-11
資料類型 article
dc.contributor 科管智財所en_US
dc.creator (作者) 鄭至甫zh_TW
dc.creator (作者) Jeng, Jyh‐Fuen_US
dc.date (日期) 2009en_US
dc.date.accessioned 7-Nov-2014 16:02:31 (UTC+8)-
dc.date.available 7-Nov-2014 16:02:31 (UTC+8)-
dc.date.issued (上傳時間) 7-Nov-2014 16:02:31 (UTC+8)-
dc.identifier.uri (URI) http://nccur.lib.nccu.edu.tw/handle/140.119/71238-
dc.description.abstract (摘要) 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.en_US
dc.format.extent 951036 bytes-
dc.format.mimetype application/pdf-
dc.language.iso en_US-
dc.relation (關聯) Lecture Notes in Computer Science, 5574, 1-11en_US
dc.subject (關鍵詞) protein sequence comparison;secondary structure element alignment;dynamic programming;length encoded profile;protein foldingen_US
dc.title (題名) Length Encoded Secondary Structure Profile for Remote Homologous Protein Detectionen_US
dc.type (資料類型) articleen