18S rRNA Alignments

Diane Stothard dstothar at magnus.acs.ohio-state.edu
Wed May 25 09:00:09 EST 1994

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 


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