Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design.

ABSTRACT: Understanding the structural repertoire of RNA is crucial for RNA genomics research. Yet current methods for finding novel RNAs are limited to small or known RNA families. To expand known RNA structural motifs, we develop a two-dimensional graphical representation approach for describing and estimating the size of RNA's secondary structural repertoire, including naturally occurring and other possible RNA motifs. We employ tree graphs to describe RNA tree motifs and more general (dual) graphs to describe both RNA tree and pseudoknot motifs. Our estimates of RNA's structural space are vastly smaller than the nucleotide sequence space, suggesting a new avenue for finding novel RNAs. Specifically our survey shows that known RNA trees and pseudoknots represent only a small subset of all possibl

SUBMITTER: Gan HH 

PROVIDER: S-EPMC156709 | biostudies-literature | 2003 Jun

REPOSITORIES: biostudies-literature