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

• Autorzy: Singh N. , Sharma S. D. , Yennamalli R. M.

Identyfikatory

DOI

10.1515/bams-2017-0023

• Języki publikacji: EN

Abstrakty

EN

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.

Słowa kluczowe

EN

microRNA; miRNA; modified S-transform; RNA sequences; secondary structure elements

• Wydawca: Uniwersytet Jagielloński - Collegium Medicum ; Index Copernicus Sp. z o.o.
• Czasopismo: Bio-Algorithms and Med-Systems
• Rocznik: 2017
• Tom: Vol. 13, no. 4
• Strony: 182--193
• Opis fizyczny: Bibliogr. 18 poz., rys., tab.

Twórcy

autor

Singh N.

• Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh 173234, India

autor

Sharma S. D.

• Department of Electronics and Communication Engineering, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh 173234, India

autor

Yennamalli R. M.

• Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh 173234, India

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