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RNA Structural Homology Search with a Succinct Stochastic Grammar Model

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Abstract

An increasing number of structural homology search tools, mostly based on profile stochastic context-free grammars (SCFGs) have been recently developed for the non-coding RNA gene identification. SCFGs can include statistical biases that often occur in RNA sequences, necessary to profile specific RNA structures for structural homology search. In this paper, a succinct stochastic grammar model is introduced for RNA that has competitive search effectiveness. More importantly, the profiling model can be easily extended to include pseudoknots, structures that are beyond the capability of profile SCFGs. In addition, the model allows heuristics to be exploited, resulting in a significant speed-up for the CYK algorithm-based search.

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Authors and Affiliations

  1. Department of Computer Science, University of Georgia, Athens, GA30602, U.S.A.

    Ying-Lei Song, Ji-Zhen Zhao, Chun-Mei Liu, Kan Liu & Li-Ming Cai

  2. Department of Plant Biology, University of Georgia, Athens, GA30602, U.S.A.

    Russell Malmberg

Authors
  1. Ying-Lei Song
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  2. Ji-Zhen Zhao
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  3. Chun-Mei Liu
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  4. Kan Liu
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  5. Russell Malmberg
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  6. Li-Ming Cai
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Correspondence to Ying-Lei Song.

Additional information

Ying-Lei Song received his B.S. degree in physics from Tsinghua University in 1998, and his M.S. degree in computer science from Ohio University in 2003. He is at present a Ph.D. candidate in the Department of computer science at University of Georgia. His research interests concentrate on designing efficient algorithms for predicting and studying secondary and tertairy structures of RNAs and proteins.

Ji-Zhen Zhao received his M.S. degree in Biology from Peking University in 1997. He is currently a Ph.D. candidate in the Department of computer science at University of Georgia. His research interests focus on modeling of RNA secondary structures and biological networks.

Chun-Mei Liu received his B.E. and M.E. degrees in Computer science and engineering from Anhui University in 1999 and 2002 respectivehex ly. She is currently a Ph.D. candidate in the Department of computer science at University of Georgia. Her research interests include secondary tertairy structures of RNAs and proteins, graph theory, and theory of computation.

Kan Liurecived his B.S. degree in engineering machanics from Beijing Institute of technology, Chaina, in 1995 and his M.S. degree in computers cience form the University of Georgia in 2004. He is a Ph.D. candidate in the University of California, Riverside. His research focuses on developing efficient algorithems and softwarefor computational problems in molecular biologyand genomics.

Ressell L. Malmberg is a professor in the Plant Biology Department, Univesity of Georgia, USA. He recived his Ph.D. degreefrom the University of Wisconsin in Genetics, then did postdoctoral work at Michigan State University and Cold Spring Harbor Laboratory, before moving to the University of Georgia. His Current research interests are in bioinformatics and in evolutionary genetics.

Li-Ming Cai is an associate professor in the Department of Computer Science at University of Georgia. He received his Ph.D. degree in computer science from Texas A & M University in 1994. He also holds B.s and M.s degrees in computer science awarded by Tsinghua University. His current research interestsinclude algorithems, computational biology, and theory of computation.

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Song, YL., Zhao, JZ., Liu, CM. et al. RNA Structural Homology Search with a Succinct Stochastic Grammar Model. J Comput Sci Technol 20, 454–464 (2005). https://doi.org/10.1007/s11390-005-0454-x

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  • DOI: https://doi.org/10.1007/s11390-005-0454-x

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