TBI-Preprint 04-01-001
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Titel:
Prediction of Consensus RNA Secondary Structures Including Pseudoknots
Author(s):
Christina Witwer,
Ivo L. Hofacker,
Peter F. Stadler
Appeared in:
IEEE/ACM Trans.\ Comp.\ Biol.\ Bioinf., 1, 66-77, (2004)
Abstract:
Most functional RNA molecules have characteristic structures that are
highly conserved in evolution. Many of them contain pseudoknots. Here we
present a method for computing the consensus structures including
pseudoknots based on alignments of a few sequences. The algorithm combines
thermodynamic and covariation information to assign scores to all possible
base pairs, the base pairs are chosen with the help of the maximum
weighted matching algorithm. We applied our algorithm to five different
types of RNA known to contain pseudoknots. All pseudoknots were predicted
correctly, and more than 85% of the base pairs were identified.
Keywords:
RNA secondary structure,
pseudoknots,
covariance scores
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Last modified: 2004-10-28 14:02:22 ivo