RNA secondary structure

Samuel J Mitchell samuelm at selway.umt.edu
Fri Jan 27 12:08:40 EST 1995


There's lots of great stuff on both small and large ribosomal subunits
(Postscript output of structures) at rdp.life.uiuc.edu
See:
Gutell, R.R., M.W. Gray, and M.N. Schnare, 1993.  A compilation of 
large subunit (23S and 23S-like) ribosomal RNA structures: 1993, Nuc. 
Acids Res., (21)13 3055-3074.

You might also look at the loopDloop (Macintosh) program by D. Gilbert - try
ftp.bio.indiana.edu:/molbio/loopdloop

Finally, two good references to some other methods are:

Eddy, S.R., and R. Durbin, 1994.  RNA sequence analysis using covariance 
models, Nucleic Acids Research, (22)11  2079-2088

Gutell, R.R., and C.R. Woese, 1990.  Higher order structural elements in 
ribosomal RNAs: Pseudo-knots and the use of noncanonical pairs, Proc. 
Natl. Acad. Sci. USA, (87) 663-667.



These ref's were all given to me by various people on the net when our 
lab began searching for better folding methods - thanks to all who 
responded, and my apologies if the ref's are incomplete!

- Sam Mitchell
(samuelm at selway.umt.edu)






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