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Tandem repeats detection in DNA sequences using Kaiser window based adaptive S-transform

Sharma S. D., Saxena R., Sharma S. N.

Bio-Algorithms and Med-Systems

2017

Vol. 13, no. 3

167--173

In computational biology the development of algorithms for the identification of tandem repeats in DNA sequences is a challenging problem. Tandem repeats identification is helpful in gene annotation, forensics, and the study of human evolution. In this work a signal processing algorithm based on adaptive S-transform, with Kaiser window, has been proposed for the exact and approximate tandem repeats detection. Usage of Kaiser window helped in identifying short as well as long tandem repeats. Thus, the limitation of earlier S-transform based algorithm that identified only microsatellites has been alleviated by this more versatile algorithm. The superiority of this algorithm has been established by comparative simulation studies with other reported methods.

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

Singh N., Sharma S. D., Yennamalli R. M.

Bio-Algorithms and Med-Systems

2017

Vol. 13, no. 4

182--193

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.

Generalized integration operators from Bloch type spaces to weighted BMOA spaces

Sharma S. D., Sharmat A.

Demonstratio Mathematica

2011

Vol. 44, nr 2

373--390

In this paper, we consider a generalized integration operator (…) induced by holomorphic maps g and φ of the open unit disk D, where φ(D) ⊂ D and n is a positive integer. We characterize boundedness and compactness of (…) from Bloch type spaces to weighted BMOA spaces by using logarithmic Carleson measure characterization of the weighted BMOA spaces.