Please use this identifier to cite or link to this item:
https://ah.lib.nccu.edu.tw/handle/140.119/86641
DC Field | Value | Language |
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dc.contributor | 資科系 | - |
dc.creator | Chang, Jia-Ming | - |
dc.creator | 張家銘 | zh_TW |
dc.creator | Notredame, Cedric | en_US |
dc.creator | Taly, Jean-François | en_US |
dc.creator | Tommaso, Paolo Di | en_US |
dc.date | 2012 | - |
dc.date.accessioned | 2016-04-27T07:30:28Z | - |
dc.date.available | 2016-04-27T07:30:28Z | - |
dc.date.issued | 2016-04-27T07:30:28Z | - |
dc.identifier.uri | http://nccur.lib.nccu.edu.tw/handle/140.119/86641 | - |
dc.description.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. | - |
dc.format.extent | 884726 bytes | - |
dc.format.mimetype | application/pdf | - |
dc.relation | BMC Bioinformatics, 13, Suppl4, S1, 1-7 | - |
dc.title | Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee | - |
dc.type | article | - |
dc.identifier.doi | 10.1186/1471-2105-13-S4-S1 | - |
dc.doi.uri | http://dx.doi.org/10.1186/1471-2105-13-S4-S1 | - |
item.grantfulltext | restricted | - |
item.openairetype | article | - |
item.openairecristype | http://purl.org/coar/resource_type/c_18cf | - |
item.cerifentitytype | Publications | - |
item.fulltext | With Fulltext | - |
Appears in Collections: | 期刊論文 |
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