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RScan: fast searching structural similarities for structured RNAs in large databases.
1MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST/Department of Automation, Tsinghua University, Beijing, China. xuechenghai@tsinghua.edu.cn
BMC Genomics
|August 1, 2007
Summary
RNA structural alignment is crucial for identifying conserved elements. The RScan algorithm significantly accelerates searching for structured RNAs in large genomic databases, outperforming existing methods for faster discovery.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Many RNA molecules exhibit conserved secondary structures rather than primary sequences.
- Identifying these conserved structures and motifs is vital for understanding RNA function.
- Current structural alignment methods are too slow for large-scale genomic database searches.
Purpose of the Study:
- To develop a fast structural alignment algorithm for searching structured RNA sequences in large genomic databases.
- To address the limitations of existing slow methods in handling large-scale queries.
Main Methods:
- The RScan algorithm was developed by combining hashing and local alignment techniques.
- RScan was tested for its speed in searching structured RNAs within genomic datasets.
Main Results:
- RScan demonstrated significantly faster search times compared to the RSEARCH method for tRNA and rRNA.
- For example, RScan searched tRNA and rRNA in the A. pernix genome in 256 and 832 seconds, respectively, versus 3,178 and 8,951 seconds for RSEARCH.
- RScan efficiently searched for microRNA precursors in human chromosome 21 in under 4 minutes.
Conclusions:
- RScan is a highly efficient tool for searching structural similarities of structured RNAs in large databases.
- The speed and accuracy of RScan make it suitable for real-world applications.
- The RScan software is publicly available for use.
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