In article <CqD8Hu.1G3 at gpu.utcc.utoronto.ca>,
L.A. Moran <lamoran at gpu.utcc.utoronto.ca> wrote:
>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
It is important to keep in mind the difference between rRNA genes and
protein coding genes. THe primary structure of the rRNA gene is a
nucleotide seqeunce and the interaction between primary and secondary
structure is direct. Protein genes are translated into another medium.
Here the phenotypic secondary structure is determined by teh resulting
amino acid sequence.