政大機構典藏-National Chengchi University Institutional Repository(NCCUR):Item 140.119/86641

English | 正體中文 | 简体中文 | Post-Print筆數 : 27 | Items with full text/Total items : 109952/140887 (78%)
Visitors : 46300252 Online Users : 1749

RC Version 6.0 © Powered By DSPACE, MIT. Enhanced by NTU Library IR team.

Home ‧ Login ‧ Upload ‧ Help ‧ About ‧ Administer

政大機構典藏 > 資訊學院 > 資訊科學系 > 期刊論文 > Item 140.119/86641

Please use this identifier to cite or link to this item: https://nccur.lib.nccu.edu.tw/handle/140.119/86641

Title:	Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee
Authors:	Chang, Jia-Ming 張家銘 Notredame, Cedric Taly, Jean-François Tommaso, Paolo Di
Contributors:	資科系
Date:	2012
Issue Date:	2016-04-27 15:30:28 (UTC+8)
Abstract:	Background: Transmembrane proteins (TMPs) constitute about 20~30% of all protein coding genes. The relative lack of experimental structure has so far made it hard to develop specific alignment methods and the current state of the art (PRALINE™) only manages to recapitulate 50% of the positions in the reference alignments available from the BAliBASE2-ref7. Methods: We show how homology extension can be adapted and combined with a consistency based approach in order to significantly improve the multiple sequence alignment of alpha-helical TMPs. TM-Coffee is a special mode of PSI-Coffee able to efficiently align TMPs, while using a reduced reference database for homology extension. Results: Our benchmarking on BAliBASE2-ref7 alpha-helical TMPs shows a significant improvement over the most accurate methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. We also estimated the influence of the database used for homology extension and show that highly non-redundant UniRef databases can be used to obtain similar results at a significantly reduced computational cost over full protein databases. TMCoffee is part of the T-Coffee package, a web server is also available from http://tcoffee.crg.cat/tmcoffee and a freeware open source code can be downloaded from http://www.tcoffee.org/Packages/Stable/Latest.
Relation:	BMC Bioinformatics, 13, Suppl4, S1, 1-7
Data Type:	article
DOI 連結:	http://dx.doi.org/10.1186/1471-2105-13-S4-S1
DOI:	10.1186/1471-2105-13-S4-S1
Appears in Collections:	[資訊科學系] 期刊論文

Files in This Item:

File	Description	Size	Format
1-7.pdf		863Kb	Adobe PDF2	710	View/Open

社群 sharing

著作權政策宣告 Copyright Announcement

1.本網站之數位內容為國立政治大學所收錄之機構典藏，無償提供學術研究與公眾教育等公益性使用，惟仍請適度，合理使用本網站之內容，以尊重著作權人之權益。商業上之利用，則請先取得著作權人之授權。
The digital content of this website is part of National Chengchi University Institutional Repository. It provides free access to academic research and public education for non-commercial use. Please utilize it in a proper and reasonable manner and respect the rights of copyright owners. For commercial use, please obtain authorization from the copyright owner in advance.

2.本網站之製作，已盡力防止侵害著作權人之權益，如仍發現本網站之數位內容有侵害著作權人權益情事者，請權利人通知本網站維護人員(nccur@nccu.edu.tw)，維護人員將立即採取移除該數位著作等補救措施。
NCCU Institutional Repository is made to protect the interests of copyright owners. If you believe that any material on the website infringes copyright, please contact our staff(nccur@nccu.edu.tw). We will remove the work from the repository and investigate your claim.

Loading...