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

TLDR

Multiple sequence alignment of biological sequences is essential for inferring homology, but nucleotide alignments are less accurate than amino‑acid alignments because codons evolve as triplets and similarity decays faster at the DNA level. TranslatorX is a web server that aligns protein‑coding nucleotide sequences guided by their amino‑acid translations. It supports all genetic codes, allows per‑sequence code assignment, integrates several alignment programs, translates ambiguous codons, cleans alignments with a protein‑based GBlocks criterion, and outputs Jalview visualizations, codon‑colored alignments, compositional bias metrics, and codon‑position‑specific alignments. The server is freely available at http://translatorx.co.uk.

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.