Rasmus Wernersson and Anders Gorm Pedersen.
RevTrans - Constructing alignments of coding DNA from aligned amino acid sequences.
Nucl. Acids Res., 2003, 31(13), 3537-3539.
Rasmus Wernersson: firstname.lastname@example.org
- Anders Gorm Pedersen: email@example.com
The simple fact that proteins are built from 20 amino acids while DNA
only contains four different bases, means that the 'signal-to-noise
ratio' in protein sequence alignments is much better than in alignments
of DNA. Besides this information-theoretical advantage, protein
alignments also benefit from the information that is implicit in
empirical substitution matrices such as BLOSUM-62.
Taken together with the generally higher rate of synonymous mutations
over non-synonymous ones, this means that the phylogenetic signal
disappears much more rapidly from DNA sequences than from the encoded
proteins. It is therefore preferable to align coding DNA at the amino
acid level and it is for this purpose we have constructed the program
RevTrans constructs a multiple DNA alignment by: (i) translating the
DNA; (ii) aligning the resulting peptide sequences; and (iii) building
a multiple DNA alignment by 'reverse translation' of the aligned
protein sequences. In the resulting DNA alignment, gaps occur in groups
of three corresponding to entire codons, and analogous codon positions
are therefore always lined up. These features are useful when
constructing multiple DNA alignments for phylogenetic analysis.
RevTrans also accepts user-provided protein alignments for greater
control of the alignment process.
Anders Gorm Pedersen,