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Title:	Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee
Authors:	張家銘 Chang, Jia-Ming Notredame, Cedric Taly, Jean-François Tommaso, Paolo Di
Contributors:	資科系
Date:	2012-03
Issue Date:	2016-05-30 17:23:31 (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. TM-Coffee 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, Vol.13, No.Suppl 4, pp.S1
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

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