A method for rapid similarity analysis of RNA secondary structures.
BACKGROUND
Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures.


RESULTS
Three sets of real data have been used as input for the example applications. Set I includes the structures from 5S rRNAs. Set II includes the secondary structures from RNase P and RNase MRP. Set III includes the structures from 16S rRNAs. Reasonable phylogenetic trees are derived for these three sets of data by using our method. Moreover, our program runs faster as compared to some existing ones.


CONCLUSIONS
The famous Lempel-Ziv algorithm can efficiently extract the information on repeated patterns encoded in RNA secondary structures and makes our method an alternative to analyze the similarity of RNA secondary structures. This method will also be useful to researchers who are interested in evolutionary analysis.
Liu
Na
N
Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, China. liunasophia@163.com
Wang
Tianming
T
D000465:Algorithms; D020029:Base Pairing; D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology; D003198:Computer Simulation; D030561:Databases, Nucleic Acid; D003663:Decision Trees; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid; D012986:Software Validation; D013997:Time Factors
D012313:RNA