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

By Federico Abascal, Rafael Zardoya, Maximilian J. Telford. Nucleic Acids Res., 2010

1,351 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d9f8f50f0010383c63e06ba8290ec60d9e37b0c7

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Citations in the corpus

Higher‐level phylogeny and evolutionary history of Pentatomomorpha (Hemiptera: Heteroptera) inferred from mitochondrial genome sequences (2019, methodology): “…Society, Systematic Entomology, 44, 810–819 Protein-coding genes were individually aligned using codon-based multiple alignments under the mafft algorithm (Katoh et al., 2005) implemented in the translatorx online platform with the L-INS-i strategy and default settings (Abascal et al., 2010).”
ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. (2012, methodology): “Several tools have been developed to automate back-translated nucleotide alignments of protein-coding sequences [11–15].”
Pitfalls in supermatrix phylogenomics (2017, neutral): “This strategy is implemented in transAlign (Bininda-Emonds 2005), TranslatorX (Abascal et al. 2010), and Seaview 4 (Gouy et al. 2010), for example.”
FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies (2014, methodology): “Software like SequenceMatrix [39], TranslatorX [40], and CONCATENATOR [41] are pure concatenation tools which can be used only via graphical user interface or which are web server designed and therefore cannot be implemented in automatic process pipelines.”
Using PhyloSuite for molecular phylogeny and tree‐based analyses (2023, methodology): “The algorithm of codon alignment implemented in PhyloSuite is similar to the one in MEGA [21] and TranslatorX [22].”
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.”