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


CONCLUSIONS
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.
MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST/Department of Automation, Tsinghua University, Beijing, China. xuechenghai@tsinghua.edu.cn
Chenghai
C
Xue
Guo-Ping
GP
Liu
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D002877:Chromosomes, Human / Q000737:chemistry; D030561:Databases, Nucleic Acid; D001330:Electronic Data Processing; D006801:Humans; D035683:MicroRNAs / Q000032:analysis / Q000737:chemistry; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000032:analysis* / Q000737:chemistry; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid
D035683:MicroRNAs; D012313:RNA