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

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Item Type:Article
Title:PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
Creators Name:Suyama, M. and Torrents, D. and Bork, P.
Abstract: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.
Keywords:Codon, Exons, Internet, Sequence Alignment, DNA Sequence Analysis, Protein Sequence Analysis, Software, User-Computer Interface
Source:Nucleic Acids Research
Publisher:Oxford University Press
Number:Web Server Issue
Page Range:W609-W612
Date:1 July 2006
Official Publication:https://doi.org/10.1093/nar/gkl315
PubMed:View item in PubMed

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