Fine-tuning structural RNA alignments in the twilight zone.

ABSTRACT:

Background

A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably.

Results

Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment foldi

SUBMITTER: Bremges A 

PROVIDER: S-EPMC2876130 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature