Accessible Requires Authentication Published by De Gruyter December 23, 2017

Modified S-transform as a tool to identify secondary structure elements in RNA

Nancy Singh, Sunil Datt Sharma and Ragothaman M. Yennamalli ORCID logo

Abstract

In this article, we describe the applicability of a signal processing method, specifically the modified S-transform (MST) method, on RNA sequences to identify periodicities between 2 and 11. MicroRNAs (miRNA) are associated with gene regulation and gene silencing and thus have wide applications in biological sciences. Also, the functionality of miRNA is highly associated with its secondary structures (stem, bulge and loop). Signal processing methods have been previously applied on genomic data to reveal the periodicities that determine a wide variety of biological functions, ranging from exon detection to microsatellite identification in DNA sequences. However, there has been less focus on RNA-based signal processing. Here, we show that the signal processing method can be successfully applied to miRNA sequences. We observed that these periodicities are highly correlated with the secondary structure of miRNA and such methods could possibly be used as indicators of secondary and tertiary structure formation.

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: None declared.

  3. Employment or leadership: None declared.

  4. Honorarium: None declared.

  5. Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication.

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Supplemental Material:

The online version of this article offers supplementary material (https://doi.org/10.1515/bams-2017-0023).

Received: 2017-10-26
Accepted: 2017-11-23
Published Online: 2017-12-23
Published in Print: 2017-12-20

©2017 Walter de Gruyter GmbH, Berlin/Boston