Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee.
BMC Bioinformatics
; 13 Suppl 4: S1, 2012 Mar 28.
Article
en En
| MEDLINE
| ID: mdl-22536955
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.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Alineación de Secuencia
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Drosophila
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Drosophila melanogaster
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Proteínas de la Membrana
Límite:
Animals
Idioma:
En
Revista:
BMC Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2012
Tipo del documento:
Article
País de afiliación:
España