| dc.contributor | 資科系 | - |
| dc.creator (作者) | 張家銘 | zh_TW |
| dc.creator (作者) | Chang, Jia-Ming | - |
| dc.creator (作者) | Notredame, Cedric | en_US |
| dc.creator (作者) | Taly, Jean-François | en_US |
| dc.creator (作者) | Tommaso, Paolo Di | en_US |
| dc.date (日期) | 2012-03 | - |
| dc.date.accessioned | 30-May-2016 17:23:31 (UTC+8) | - |
| dc.date.available | 30-May-2016 17:23:31 (UTC+8) | - |
| dc.date.issued (上傳時間) | 30-May-2016 17:23:31 (UTC+8) | - |
| dc.identifier.uri (URI) | http://nccur.lib.nccu.edu.tw/handle/140.119/97009 | - |
| dc.description.abstract (摘要) | 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. | - |
| dc.format.extent | 838056 bytes | - |
| dc.format.mimetype | application/pdf | - |
| dc.relation (關聯) | BMC Bioinformatics, Vol.13, No.Suppl 4, pp.S1 | - |
| dc.title (題名) | Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee | - |
| dc.type (資料類型) | article | - |
| dc.identifier.doi (DOI) | 10.1186/1471-2105-13-S4-S1 | - |
| dc.doi.uri (DOI) | http://dx.doi.org/10.1186/1471-2105-13-S4-S1 | - |
