An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast.

ABSTRACT:

Background

Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for taking structural conservation into account. Although many sophisticated algorithms for the purpose have been proposed to date, further improvement in efficiency is necessary to accelerate its large-scale applications including non-coding RNA (ncRNA) discovery.

Results

We developed a new genetic algorithm, Cofolga2, for simultaneously computing pairwise RNA sequence alignment and consensus folding, and benchmarked it using BRAliBase 2.1. The benchmark results showed that our new algorithm is accurate and efficient in both time and memory usage. Then, combining with the originally trained SVM, we applied

SUBMITTER: Taneda A 

PROVIDER: S-EPMC2630964 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature