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

Chenghai Xue,Guo-Ping Liu

doi:10.1186/1471-2164-8-257

Abstract

BackgroundMany 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.ResultsAn 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.ConclusionThese 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 .

Highlights

Many RNAs have evolutionarily conserved secondary structures instead of primary sequences
We used the tRNA family as an example to explain the filtering criteria
P-values of the free energies of the secondary structures were calculated based on each sequence and their 1000 shuffling sequences with invariable dinucleotide frequency

Summary

Introduction

Many RNAs have evolutionarily conserved secondary structures instead of primary sequences. 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 wide range of RNA molecules can form specific secondary structures by folding their primary sequences. The secondary structures of many non-coding RNAs (ncRNA), like the cloverleaf structure of tRNA and the hairpin structure of microRNA precursor (pre-miRNA), have been evolutionarily conserved instead of the primary sequences [3]. Several computational methods have been reported to find these conserved secondary structures, as well as common local structural motifs in pair-wise or multiple sequences. The local structures or structural motifs of RNA molecules (page number not for citation purposes)

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