Ruslan A Soldatov1, Svetlana V Vinogradova, Andrey A Mironov. 1. Institute for Information Transmission Problems (the Kharkevich Institute), Russian Academy of Sciences, 19 Bolshoy Karetny per., Moscow 127994 and Department of Bioengineering and Bioinformatics, Moscow State University, 1-73 Vorobyevy Gory, Moscow 119991, Russia.
Abstract
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.
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.
Authors: Katrina M Kutchko; Emily A Madden; Clayton Morrison; Kenneth S Plante; Wes Sanders; Heather A Vincent; Marta C Cruz Cisneros; Kristin M Long; Nathaniel J Moorman; Mark T Heise; Alain Laederach Journal: Nucleic Acids Res Date: 2018-04-20 Impact factor: 16.971
Authors: Emily A Madden; Alain Laederach; Nathanial J Moorman; Mark T Heise; Kenneth S Plante; Clayton R Morrison; Katrina M Kutchko; Wes Sanders; Kristin M Long; Sharon Taft-Benz; Marta C Cruz Cisneros; Ashlyn Morgan White; Sanjay Sarkar; Grace Reynolds; Heather A Vincent Journal: J Virol Date: 2020-11-23 Impact factor: 5.103