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This article is part of the supplement: Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Bioinformatics

Open Access Proceedings

Efficient known ncRNA search including pseudoknots

Cheng Yuan and Yanni Sun*

Author Affiliations

Department of Computer Science and Engineering Michigan State University East Lansing, MI, 48824, USA

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BMC Bioinformatics 2013, 14(Suppl 2):S25  doi:10.1186/1471-2105-14-S2-S25

Published: 21 January 2013



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.


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 test our tool on a contiguous 22-Mb region of the Maize Genome. The experimental results show that our work competes favorably with other pseudoknot search methods.


Our sub-structure based tool can conduct genome-scale pseudoknot-containing ncRNA search effectively and efficiently. It provides a complementary pseudoknot search tool to Infernal. The source codes are available at webcite.