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

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 leve...

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Detalles Bibliográficos
Autores principales: Suyama, Mikita, Torrents, David, Bork, Peer
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538804/
https://www.ncbi.nlm.nih.gov/pubmed/16845082
http://dx.doi.org/10.1093/nar/gkl315
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author Suyama, Mikita
Torrents, David
Bork, Peer
author_facet Suyama, Mikita
Torrents, David
Bork, Peer
author_sort Suyama, Mikita
collection PubMed
description 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 .
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spelling pubmed-15388042006-08-18 PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments Suyama, Mikita Torrents, David Bork, Peer Nucleic Acids Res Article 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 . Oxford University Press 2006-07-01 2006-07-14 /pmc/articles/PMC1538804/ /pubmed/16845082 http://dx.doi.org/10.1093/nar/gkl315 Text en © The Author 2006. Published by Oxford University Press. All rights reserved
spellingShingle Article
Suyama, Mikita
Torrents, David
Bork, Peer
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
title PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
title_full PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
title_fullStr PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
title_full_unstemmed PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
title_short PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
title_sort pal2nal: robust conversion of protein sequence alignments into the corresponding codon alignments
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538804/
https://www.ncbi.nlm.nih.gov/pubmed/16845082
http://dx.doi.org/10.1093/nar/gkl315
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