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Bioinformatics Advance Access published online on January 2, 2008
Bioinformatics, doi:10.1093/bioinformatics/btm636
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins

Walter Pirovano 1, K. Anton Feenstra 1 and Jaap Heringa 1,*

1Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands

*To whom correspondence should be addressed. Dr. Jaap Heringa, E-mail: heringa{at}cs.vu.nl


  Abstract

Motivation: Membrane-bound proteins are a special class of proteins. The regions that insert into the cell-membrane have a profoundly different hydrophobicity pattern compared to soluble proteins. Multiple alignment techniques use scoring schemes tailored for sequences of soluble proteins and are therefore in principle not optimal to align membrane-bound proteins.

Results: Transmembrane regions in protein sequences can be reliably recognized using state-of-the-art sequence prediction techniques. Furthermore, membrane-specific scoring matrices are available. We have developed a new alignment method, called PRALINETM, which integrates these two features to enhance multiple sequence alignment. We tested our algorithm on the transmembrane alignment benchmark set by Bahr et al. (Bahr, et al., 2001), and show that the quality of transmembrane alignments can be significantly improved compared to the quality produced by a standard multiple alignment technique. The results clearly indicate that the incorporation of these new elements into current state-of-the-art alignment methods is crucial for optimizing the alignment of transmembrane proteins.

Availability: A webserver is available at http://www.ibi.vu.nl/programs/pralinewww.

Associate Editor: Prof. Burkhard Rost

Received on November 20, 2007; revised on December 20, 2007; accepted on December 21, 2007

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