title: TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations.
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.
authors.affiliation: Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal, 2, 28006 Madrid, Spain.
authors.forename: Federico
authors.initials: F
authors.lastname: Abascal
authors.forename: Rafael
authors.initials: R
authors.lastname: Zardoya
authors.forename: Maximilian J
authors.initials: MJ
authors.lastname: Telford
mesh_terms: D005815:Genetic Code; D020407:Internet; D010802:Phylogeny; D014176:Protein Biosynthesis; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein; D012984:Software