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Use of secondary structure in alignments

David A. Kirby dkirby at csc.umd.edu
Tue May 21 11:59:28 EST 1996

Diane Stothard (dstothar at magnus.acs.ohio-state.edu) wrote:

: I was wondering what the consensus feeling is in this group for using secondary
: structure as a guide for aligning rRNA gene sequences. I personally feel it is
: necessary in order to insure comparison of homologous sites, but I have met
: many people that do not believe in secondary structures and therefore, align
: their sequences randomly (i.e., by base letter). I would especially appreciate
: responses from people that design phylogenetic software or people that work on
: the development of secondary structure models.

: Thanks!
: Diane

I would suggest the following papers which dsicuss a progressive sequence 
alignement, which utilizes information about puttative secondary structures to 
refine a sequence alignemt.

JAMES, B. D., G. J. OLSEN, J. LIU and N.R. PACE, 1988  The secondary structure 
of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme. Cell 52: 19-26.

KIRBY, D. A., S. V. MUSE and W. STEPHAN, 1995  Maintenance of pre-mRNA secondary structure by epistatic selection. Proc Natl Acad Sci USA 92: 9047-9051.

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