Why to convert protein msa into nucleotide msa?

Answer 1

Hi

Genetic information can be obtained at different levels namely genomic DNA, RNA and protein.. another level, CDS (Coding sequence;actually part of mRNA) can be sometimes more informative than all above in the way that being 'inframe' DNA (more correctly cDNA) it can be directly converted to protein.. Such sequences can be obtained from of protein msa converted into nucleotide msa. This job cannot be done the usual way and requires aligned protein msa to be reverse translated to nucleotide msa (unaligned CDS is necessary to account for genetic redundancy and aligned protein msa is needed to preserve codon integrity and prevent alignment artefact ;gaps should be multiples of 3). Such sequences are often studied in context of molecular evolution e.g estimating nonsynonymous and synonymous substitutions in branches of phylogenetic tree..

HTH

Cheers,

Sunil

Answer 2

Converting protein multiple sequence alignments (MSAs) into nucleotide MSAs can help identify non-synonymous and synonymous mutations, providing insights into protein evolution and function. Nucleotide MSAs can reveal codon usage patterns, conservation, and selection pressures that may not be apparent in protein sequences alone. Additionally, nucleotide MSAs are useful for studying genetic diversity, gene expression regulation, and molecular evolution.