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.
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.