Here are a couple of Internet resources for rRNA which may be of
interest to your topic:
Gopher to rdpgopher.life.uiuc.edu for the Ribosomal Database project
archive. This archive includes sequences, alignments, secondary
structures and phylo trees for large and small subunit ribosomal
RNA from many species. This is the work of (& citation for):
Niels Larsen, Gary J. Olsen, Bonnie L. Maidak, Michael J.
McCaughey, Ross Overbeek, Thomas J. Macke, Terry L. Marsh
and Carl R. Woese: The ribosomal database project. _Nucleic
Acids Research_, Vol. 21 Supplement, p.3021-3023, 1993.
Gopher or ftp to ftp.bio.indiana.edu:/molbio/rnase-p for the
ribonuclease P sequence database archive, including a compilation of
sequences, sequence alignments, secondary structures, and other
information. This is the work of James W. Brown, Elizabeth Haas,
and Norman Pace.
I know that Pace's lab here uses secondary structure information
in making alignments. I couldn't give you any details on it
though. The RDP project produces a number of alignments, which
I think take into account secondary structures. The ref above
and at the archive may include details.
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu