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

By M. Suyama, D. Torrents, Peer Bork. Nucleic Acids Res., 2006

3,105 citations recorded by the source corpus.

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 .

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d24f3d78309a46693b01bbb356ed0e361b011b40

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Citations in the corpus

Class of multiple sequence alignment algorithm affects genomic analysis. (2013, methodology): “Amino acid alignments were back translated into codon alignments using Pal2Nal (Suyama et al. 2006) where necessary.”
PGDD: a database of gene and genome duplication in plants (2012, methodology): “For example, Ks values between pairs of ortholog/paralog genes are determined by Clustal W (48), PAL2NAL (49) and yn00 program of the PAML package (50) in this step.”
ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. (2012, background): “We thank Mikita Suyama for the permission to modify the program PAL2NAL and Yongbing Zhao for computational assistance.”
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. (2008, methodology): “Synonymous substitution (Ks) and fourfold degenerate site transversion (4DTV) calculation For each pair of homologs, we aligned their protein sequences using CLUSTALW (Thompson et al. 1994) and converted the protein alignment to DNA alignment using PAL2NAL (Suyama et al. 2006).”
Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins (2011, methodology): “83 [86] and the alignments were reverse translated using PAL2NAL [87].”
Genome evolution across 1,011 Saccharomyces cerevisiae isolates (2018, positive): “For each orthologous group, the protein sequences across the 41 strains were aligned with MUSCLE (v.3.8.1551) 69 , and the resulting protein alignment was further used to guide the corresponding CDS alignment using PAL2NAL (v.14) 70 .”
AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential (2019, methodology): “The Dn/Ds values are averaged from codon alignments of reference organisms using Pal2Nal (36) and the PAML (37) application ‘yn00’.”
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations (2010, neutral): “All these solutions, with the exception of RevTrans, require that the user provide the amino acid alignment together with nucleotide sequences, some of the packages do not provide a complete list of available genetic codes (PAL2NAL) and, except for protal2dna, none of these tools allows the user to ”
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons (2011, methodology): “Tools such as revTrans [18], transAlign [19], PAL2NAL [20], and TranslatorX [21] were specifically developed to automate this straightforward alignment strategy.”