Computational Analysis of RNAs

Abstract

Genome sequence analysis of RNAs presents special challenges to computational biology, because conserved RNAsecondary structure plays a large part in RNA analysis. Algorithms well suited for RNA secondary structure and sequenceanalysis have been borrowed from computational linguistics. These "stochastic context-free grammar" (SCFG) algorithmshave enabled the development of new RNA genefinding and RNA homology search software. The aim of this paper is toprovide an accessible introduction to the strengths and weaknesses of SCFG methods and to describe the state of the art inone particular kind of application: SCFG-based RNA similarity searching. The INFERNAL and RSEARCH programs are capableof identifying distant RNA homologs in a database search by looking for both sequence and secondary structureconservation.