18S rRNA Alignments

Jack Kramer kramer at oj.rsmas.miami.edu
Thu May 26 07:47:21 EST 1994

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.

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