title: 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 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.
authors.affiliation: Bioinformatics and Genomics program, Centre for Genomic Regulation (CRG) and UPF, Barcelona 08003, Spain.
authors.forename: Jia-Ming
authors.initials: JM
authors.lastname: Chang
authors.forename: Paolo
authors.initials: P
authors.lastname: Di Tommaso
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Taly
authors.forename: Cedric
authors.initials: C
authors.lastname: Notredame
mesh_terms: D000465:Algorithms; D000818:Animals; D030562:Databases, Protein; D004330:Drosophila / Q000737:chemistry* / Q000378:metabolism; D004331:Drosophila melanogaster / Q000737:chemistry* / Q000378:metabolism; D008565:Membrane Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software
chemical_list: D008565:Membrane Proteins