UCL Discovery
UCL home » Library Services » Electronic resources » UCL Discovery

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

Abascal, F; Zardoya, R; Telford, MJ; (2010) TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Research , 38 (Web Se) W7-13. 10.1093/nar/gkq291. Green open access

[thumbnail of Nucl._Acids_Res.-2010-Abascal-W7-W13.pdf]
Preview
PDF
Nucl._Acids_Res.-2010-Abascal-W7-W13.pdf

Download (2MB)

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.

Type: Article
Title: TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/nar/gkq291
Publisher version: http://dx.doi.org/10.1093/nar/gkq291
Language: English
Additional information: This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: Genetic Code, Internet, Phylogeny, Protein Biosynthesis, Sequence Alignment, Sequence Analysis, DNA, Sequence Analysis, Protein, Software
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/1310555
Downloads since deposit
301Downloads
Download activity - last month
Download activity - last 12 months
Downloads by country - last 12 months

Archive Staff Only

View Item View Item