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Nucleic Acids Research 2006 34(Web Server issue):W609-W612; doi:10.1093/nar/gkl315
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

Mikita Suyama1, David Torrents1 and Peer Bork1,2,*

1 European Molecular Biology Laboratory, Meyerhofstrasse 1 D-69117 Heidelberg, Germany 2 Max Delbrück Center for Molecular Medicine, D-13092 Berlin-Buch Germany

*To whom correspondence should be addressed. Tel: +49 6221 387 8526; Fax: +49 6221 387 8517; Email addresses: bork{at}embl.de

Received April 3, 2006. Revised April 6, 2006. Accepted April 11, 2006.

PAL2NAL is a web server that constructs a multiple codon alignment from the corresponding aligned protein sequences. Such codon alignments can be used to evaluate the type and rate of nucleotide substitutions in coding DNA for a wide range of evolutionary analyses, such as the identification of levels of selective constraint acting on genes, or to perform DNA-based phylogenetic studies. The server takes a protein sequence alignment and the corresponding DNA sequences as input. In contrast to other existing applications, this server is able to construct codon alignments even if the input DNA sequence has mismatches with the input protein sequence, or contains untranslated regions and polyA tails. The server can also deal with frame shifts and inframe stop codons in the input models, and is thus suitable for the analysis of pseudogenes. Another distinct feature is that the user can specify a subregion of the input alignment in order to specifically analyze functional domains or exons of interest. The PAL2NAL server is available at http://www.bork.embl.de/pal2nal.


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