Efficient known ncRNA search including pseudoknots.

ABSTRACT:

Background

Searching for members of characterized ncRNA families containing pseudoknots is an important component of genome-scale ncRNA annotation. However, the state-of-the-art known ncRNA search is based on context-free grammar (CFG), which cannot effectively model pseudoknots. Thus, existing CFG-based ncRNA identification tools usually ignore pseudoknots during search. As a result, dozens of sequences that do not contain the native pseudoknots are reported by these tools. When pseudoknot structures are vital to the functions of the ncRNAs, these sequences may not be true members.

Results

In this work, we design a pseudoknot search tool using multiple simple sub-structures, which are derived from knot-free and bifurcation-free structural motifs in the underlying family. We

SUBMITTER: Yuan C 

PROVIDER: S-EPMC3549841 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature