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

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 .

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

“…To calculate the number of synonymous substitutions per site (Ks), ClustalW 49 alignments of paralogous and orthologous protein sequences were used to guide nucleic coding sequence alignments with PAL2NAL 50 . Ks values were calculated using the Yang-Nielson method implemented in PAML 51 .…”

Evolution of the Relaxin/Insulin-like Gene Family in Placental Mammals: Implications for Its Early Evolution

“…Nucleotide alignments were generated using the amino acid alignments as a template with the software PAL2NAL (Suyama et al 2006). Finally, the biological accuracy of alignments was assessed using the software MUMSA (Lassmann and Sonnhammer 2005), which compares alignment blocks from different alignment strategies to assess the difficulty of an alignment case, and also ranks the quality of each alternative alignment.…”

Restriction of Equine Infectious Anemia Virus by Equine APOBEC3 Cytidine Deaminases

“…All A3 sequences in the databases from mammalian species within Laurasiatheria were retrieved for analysis, as follows: Sus scrofa, A3Z2 (NM_001097446); Bos taurus, A3Z1 (EU864534), A3Z2 (NM_ 001077845), and A3Z3 (DQ974646); Ovis aries, A3Z1 (EU864543), A3Z2 (EU864535), and A3Z3 (NM_001093784); Canis lupus, A3Z3 (XM_538369) and A3Z1 (XM_847690); Felis catus, A3Z3 (NM_001112710), A3Z2a (ABW83272), A3Z2b (ABW83273), and A3Z2c (ABW83271); Lynx lynx, A3Z3 (EU007553) and A3Z2 isolate 1 (EU007546); Puma concolor, A3Z2 (EU007545); Panthera pardus, A3Z3 (EU007551) and A3Z2 (ABA62303); Panthera leo, A3Z3 (U007549), A3Z2 isolate 7 (EU007543), and A3Z2 isolate 2 (EU007544); Panthera tigris, A3Z3 (EU007550), A3Z2 (AAY99623), A3Z2 isolate 2 (EU016361), and A3Z2 isolate 3 (EU016362). The sequences were aligned at the amino acid level with MUSCLE (http://www.drive5.com/muscle/) (15,16), visualized for manual correction with Se-Al (freely distributed by Andrew Rambaut at http: //tree.bio.ed.ac.uk/software/seal/), and back-translated to the nucleotide level using PAL2NAL (http://www.bork.embl.de/pal2nal) (88). Maximum-likelihood (ML) phylogenetic analysis was performed with the program RAxML HPC (randomized accelerated maximum likelihood for high performance computing) (84,85) using the GTRϩ⌫4 model of evolution and the CAT approximation of rate heterogeneity (83), introducing three partitions that corresponded to each of the codon positions.…”