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. 2010 Jul;38(Web Server issue):W7-13.
doi: 10.1093/nar/gkq291. Epub 2010 Apr 30.

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

Federico Abascal  1 , Rafael Zardoya, Maximilian J Telford
Affiliations

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

Federico Abascal et al. Nucleic Acids Res. 2010 Jul.

Abstract

We present TranslatorX, a web server designed to align protein-coding nucleotide sequences based on their corresponding amino acid translations. Many comparisons between biological sequences (nucleic acids and proteins) involve the construction of multiple alignments. Alignments represent a statement regarding the homology between individual nucleotides or amino acids within homologous genes. As protein-coding DNA sequences evolve as triplets of nucleotides (codons) and it is known that sequence similarity degrades more rapidly at the DNA than at the amino acid level, alignments are generally more accurate when based on amino acids than on their corresponding nucleotides. TranslatorX novelties include: (i) use of all documented genetic codes and the possibility of assigning different genetic codes for each sequence; (ii) a battery of different multiple alignment programs; (iii) translation of ambiguous codons when possible; (iv) an innovative criterion to clean nucleotide alignments with GBlocks based on protein information; and (v) a rich output, including Jalview-powered graphical visualization of the alignments, codon-based alignments coloured according to the corresponding amino acids, measures of compositional bias and first, second and third codon position specific alignments. The TranslatorX server is freely available at http://translatorx.co.uk.

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Figures

Figure 1.
Figure 1.
Example illustrating the different performance of the direct and back-translated nucleotide alignments (multiple alignments were built with Muscle with default parameters).
Figure 2.
Figure 2.
Screen capture of a fragment of the results of TranslatorX. The nucleotide back-translated alignment and the corresponding amino acid alignment are shown with Jalview.
Figure 3.
Figure 3.
Comparison of the phylogenetic trees inferred from the sub-alignments that comprise positions whose alignment differed between the back-translated and direct Mafft (A, B) and Muscle (C, D) alignments.
See this image and copyright information in PMC

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