PAL2NAL

Robust conversion of protein sequence alignments into the corresponding codon alignments

Mikita Suyama, David Torrents, Peer Bork

Research output: Contribution to journalArticle

1047 Citations (Scopus)

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.

Original languageEnglish
JournalNucleic acids research
Volume34
Issue numberWEB. SERV. ISS.
DOIs
Publication statusPublished - Jul 1 2006

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Sequence Alignment
Codon
Untranslated Regions
Pseudogenes
Proteins
Terminator Codon
DNA
Exons
Nucleotides
Genes

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

PAL2NAL : Robust conversion of protein sequence alignments into the corresponding codon alignments. / Suyama, Mikita; Torrents, David; Bork, Peer.

In: Nucleic acids research, Vol. 34, No. WEB. SERV. ISS., 01.07.2006.

Research output: Contribution to journalArticle

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