Cheng Yuan1, Yanni Sun. 1. Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA. yannisun@msu.edu
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 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. CONCLUSIONS: 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 http://www.cse.msu.edu/~chengy/knotsearch.
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 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. CONCLUSIONS: 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 http://www.cse.msu.edu/~chengy/knotsearch.
Authors: Fusheng Wei; Joshua C Stein; Chengzhi Liang; Jianwei Zhang; Robert S Fulton; Regina S Baucom; Emanuele De Paoli; Shiguo Zhou; Lixing Yang; Yujun Han; Shiran Pasternak; Apurva Narechania; Lifang Zhang; Cheng-Ting Yeh; Kai Ying; Dawn H Nagel; Kristi Collura; David Kudrna; Jennifer Currie; Jinke Lin; Hyeran Kim; Angelina Angelova; Gabriel Scara; Marina Wissotski; Wolfgang Golser; Laura Courtney; Scott Kruchowski; Tina A Graves; Susan M Rock; Stephanie Adams; Lucinda A Fulton; Catrina Fronick; William Courtney; Melissa Kramer; Lori Spiegel; Lydia Nascimento; Ananth Kalyanaraman; Cristian Chaparro; Jean-Marc Deragon; Phillip San Miguel; Ning Jiang; Susan R Wessler; Pamela J Green; Yeisoo Yu; David C Schwartz; Blake C Meyers; Jeffrey L Bennetzen; Robert A Martienssen; W Richard McCombie; Srinivas Aluru; Sandra W Clifton; Patrick S Schnable; Doreen Ware; Richard K Wilson; Rod A Wing Journal: PLoS Genet Date: 2009-11-20 Impact factor: 5.917