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Open Access Software

RScan: fast searching structural similarities for structured RNAs in large databases

Chenghai Xue1* and Guo-Ping Liu23

Author Affiliations

1 MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China

2 Department of Engineering, University of Glamorgan, Pontypridd CF37 1DL, UK

3 LCSIS, Institute of Automation, CAS, Beijing 100080, China

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BMC Genomics 2007, 8:257  doi:10.1186/1471-2164-8-257

Published: 31 July 2007

Abstract

Background

Many RNAs have evolutionarily conserved secondary structures instead of primary sequences. Recently, there are an increasing number of methods being developed with focus on the structural alignments for finding conserved secondary structures as well as common structural motifs in pair-wise or multiple sequences. A challenging task is to search similar structures quickly for structured RNA sequences in large genomic databases since existing methods are too slow to be used in large databases.

Results

An implementation of a fast structural alignment algorithm, RScan, is proposed to fulfill the task. RScan is developed by levering the advantages of both hashing algorithms and local alignment algorithms. In our experiment, on the average, the times for searching a tRNA and an rRNA in the randomized A. pernix genome are only 256 seconds and 832 seconds respectively by using RScan, but need 3,178 seconds and 8,951 seconds respectively by using an existing method RSEARCH. Remarkably, RScan can handle large database queries, taking less than 4 minutes for searching similar structures for a microRNA precursor in human chromosome 21.

Conclusion

These results indicate that RScan is a preferable choice for real-life application of searching structural similarities for structured RNAs in large databases. RScan software is freely available at http://bioinfo.au.tsinghua.edu.cn/member/cxue/rscan/RScan.htm webcite.