General Information
| Description | Fast and accurate detection of locally optimal potentially structured RNA segments |
| Homepage | http://bioinf.fbb.msu.ru/RNASurface/downloads.html |
Publications
RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments
Motivation:
During the past decade, new classes of non-coding RNAs (ncRNAs) and their unexpected functions were discovered. Stable secondary structure is the key feature of many non-coding RNAs. Taking into account huge amounts of genomic data, development of computational methods to survey genomes for structured RNAs remains an actual problem, especially when homologous sequences are not available for comparative analysis. Existing programs scan genomes with a fixed window by efficiently constructing a matrix of RNA minimum free energies. A wide range of lengths of structured RNAs necessitates the use of many different window lengths that substantially increases the output size and computational efforts.
Results:
In this article, we present an algorithm RNASurface to efficiently scan genomes by constructing a matrix of significance of RNA secondary structures and to identify all locally optimal structured RNA segments up to a predefined size. RNASurface significantly improves precision of identification of known ncRNA in Bacillus subtilis.
Availability and implementation:
RNASurface C source code is available from http://bioinf.fbb.msu.ru/RNASurface/downloads.html.
Contact:
ruslansoldatov@gmail.com
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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StatAlign 2.0
Published January 2013
Combining statistical alignment with RNA secondary structure prediction
BlockClust
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Efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles
RNA structure framework
Published October 2015
Automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data
Foldalign 2.5
Published December 2015
Multithreaded implementation for pairwise structural RNA alignment
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