![]() 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. 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. 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. Besides this information-theoretical advantage, protein alignments also benefit from the information that is implicit in empirical substitution matrices such as BLOSUM-62. 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. This article has been cited by other articles in PMC.
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