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BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S1. doi: 10.1186/1471-2105-13-S4-S1.

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

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Bioinformatics and Genomics program, Centre for Genomic Regulation (CRG) and UPF, Barcelona 08003, Spain.



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 (PRALINEā„¢) only manages to recapitulate 50% of the positions in the reference alignments available from the BAliBASE2-ref7.


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.


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 PRALINEā„¢. 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 and a freeware open source code can be downloaded from

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