Nucleic Acids Research, Vol 25, Issue 8 1559-1564, Copyright © 1997 by Oxford University Press
D Gautheret and RR Gutell
The success of comparative analysis in resolving RNA secondary structure
and numerous tertiary interactions relies on the presence of base
covariations. Although the majority of base covariations in aligned
sequences is associated to Watson-Crick base pairs, many involve
non-canonical or restricted base pair exchanges (e.g. only G:C/A:U),
reflecting more specific structural constraints. We have developed a
computer program that determines potential base pairing conformations for a
given set of paired nucleotides in a sequence alignment. This program
(ISOPAIR) assumes that the base pair conformation is maintained through
sequence variation without significantly affecting the path of the
sugar-phosphate backbone. ISOPAIR identifies such 'isomorphic' structures
for any set of input base pair or base triple sequences. The program was
applied to base pairs and triples with known structures and sequence
exchanges. In several instances, isomorphic structures were correctly
identified with ISOPAIR. Thus, ISOPAIR is useful when assessing
non-canonical base pair conformations in comparative analysis. ISOPAIR
applications are limited to those cases where unusual base pair exchanges
indeed reflect a non- canonical conformation.
ARTICLES
Inferring the conformation of RNA base pairs and triples from patterns of sequence variation
Structural and Genetic Information, CNRS EP91, 31 ch. Joseph Aiguier, 13402 Marseille Cedex 20, France. gauthere@igs.cnrs-mrs.fr
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