Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee.

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 improvemen

SUBMITTER: Chang JM 

PROVIDER: S-EPMC3303701 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature