[BiO BB] RNA 3D structure codes/ splicing prediction

Mike Marchywka marchywka at hotmail.com
Thu Dec 27 17:51:42 EST 2007

I was working on a framework for generalized splicing and editing analysis
while I can across this paper,


Pre-mRNA Secondary Structure Prediction Aids Splice Site Prediction (2002)  (Make Corrections)  (3 citations)
Donald J. Patterson, Ken Yasuhara, Walter L. Ruzzo
Proceedings of the Pacific Symposium on Biocomputing

which seemed intuitively appealing but I didn't immediately find a lot of
more recent work. I guess I have three questions,

1) Is splicing still a bit of an open area or has it been "solved?"
2) Is anyone familiar with this or related work?
3) Any comments on code or papers for predicting RNA shape from sequence?
The author of this paper conclude,

"While specific structural signatures were not
detected, general trends toward helix formation in the region of the splice site suggest
the possibility of greater exploitation of structural cues by gene finding algorithms.
Similar structural biases were observed at the donor splice site in the same data
set, but not with sufficient strength that statistical significance could be ascribed to
them. Future research is warranted toward the development of models that capture
structural features at the donor splice site, as well as improving upon the acceptor site
models we have presented and their biological interpretation."

and I thought there may be some easy ways today( paper is from 2002)  to explore this idea
( If I had a model for the cavity into which the RNA had to fit this may not be
too difficult to figure out).


Mike Marchywka
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