Abstract
Given the importance of RNA secondary structures in defining their biological role, it would be convenient for researchers seeking RNA data if both sequence and structural information pertaining to RNA molecules are made available together. Current nucleotide data repositories archive only RNA sequence data. Furthermore, storage formats which can frugally represent RNA sequence as well as structure data in a single file, are currently unavailable. This article proposes a novel storage format, ‘FASTR’, for concomitant representation of RNA sequence and structure. The storage efficiency of the proposed FASTR format has been evaluated using RNA data from various microorganisms. Results indicate that the size of FASTR formatted files (containing both RNA sequence as well as structure information) are equivalent to that of FASTA-format files, which contain only RNA sequence information. RNA secondary structure is typically represented using a combination of a string of nucleotide characters along with the corresponding dot-bracket notation indicating structural attributes. ‘FASTR’ – the novel storage format proposed in the present study enables a frugal representation of both RNA sequence and structural information in the form of a single string. In spite of having a relatively smaller storage footprint, the resultant ‘fastr’ string(s) retain all sequence as well as secondary structural information that could be stored using a dot-bracket notation. An implementation of the ‘FASTR’ methodology is available for download at http://metagenomics.atc.tcs.com/compression/fastr .
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Acknowledgements
Tungadri Bose is also a PhD scholar in the Indian Institute of Technology, Bombay, and would like to acknowledge the Institute for its support. We also thank Mr Pranav Nawathe for assisting in the development of the FASTR webpage.
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Corresponding editor: Mandar V Deshmukh
[Bose T, Dutta A, Mohammed MH, Gandhi H and Mande SS 2015 FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information. J. Biosci.] DOI 10.1007/s12038-015-9546-0
Supplementary materials pertaining to this article are available on the Journal of Biosciences Website at http://www.ias.ac.in/jbiosci/sep2015/supp/Bose.pdf
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Bose, T., Dutta, A., MH, M. et al. FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information. J Biosci 40, 571–577 (2015). https://doi.org/10.1007/s12038-015-9546-0
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DOI: https://doi.org/10.1007/s12038-015-9546-0