RNA, inverted sequences, & structure?

Erik Forbes Y. Hom ehom1 at cc.swarthmore.edu
Tue Jul 19 12:53:49 EST 1994


Has anyone come across programs (that are freely available) that search out
inverted sequences of RNA?  Actually, I'm interested in determining whether
or not a mRNA sequence I have has regions through which it folds in such a
manner as to delay its translation.  If you have some good suggestions on
this subject, could you please post them on this bulletin board?  I've
tried a crude attempts to distinguish possible interactive regions using
DNAStar - but the algorithms in the package don't permit a
read-in-one-direction sequence homology comparison between a
single-stranded DNA (really the ~RNA sequence) and it's reverse compliment
strand (hence, after translating the homologous regions, I get the domains
that are complimentary).  The best attempt I've had with using this program
was not using any alignment "algorithms" at all; I simply constructed a
correlation plot (DNAPlot for any who know it) between the strand and the
reverse compliment - I get some notable regions but the resolution of the
plot (for a ~4000 nucletide sequence) is not great.  Also, I have a paper
on the stability constants of nucleotide interactions, indicating that a
G-G interaction is significantly greater than a A-U interaction, so my
original search for inverted sequences may give only a partial picture; I
figure these stability constants should be incorporated into such a
program/search to be realistic.  Futhermore, there should be a cooperative
effect that should be factored in (i.e. the interaction of one ntde to
another, although not great may increase/decrease depending on the adjacent
ntde(s) - a lowering in degrees of freedom); what would this effect look
like???

Thanks a lot in advance

erik




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