In article <2rvll9$jhu at charm.magnus.acs.ohio-state.edu>,
Diane Stothard <dstothar at magnus.acs.ohio-state.edu> wrote:
>It is ESSENTIAL to take secondary structure into account when aligning rRNA
>genes! (It should be essential when aligning any gene sequence except
>structures are not known for many proteins.) If you do not align your sequences
>based on secondary structure, you cannot verify that you are actually comparing
>homologous sites. If you are not comparing homologous sites, you cannot say
>ANYTHING about the evolutionary relationship between the sequences you are
>analyzing!
>
You are making the assumption that secondary structure is more highly conserved
than primary structure. This is only an assumption. Evolutionary relationships
are based on accumulated differences in the nucleotide sequence of homologous
genes and this affects the amino acid sequence of the protein. A mutation
(variation) could give rise to a primary sequence that results in an altered
secondary structure. That variation could become fixed in the population if
the changed secondary structure is not selected against. Two proteins can
have similar amino acid sequences but different secondary structures in some
regions.
There are several examples of proteins that have similar secondary structures
but are not homologous - or at least do not seem to have a common ancestor.
Laurence A. Moran (Larry)
