Title: Computation of entropy and energetics profiles of a single-stranded viral DNA

Authors: Perambur S. Neelakanta, Sharmistha Chatterjee, George A. Thengum-Pallil

Addresses: Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431, USA. ' Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431, USA. ' Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431, USA

Abstract: The bioinformatic aspects of computing entropy and energetic profiles associated with a viral single-stranded DNA (ssDNA) are addressed. The analyses envisaged thereof determine the structural (stem and loop) features, identify the CpG motifs and delineate the boundaries of coding DNA segments along a test viral (B19) ssDNA. The analytical modelling and computational efforts conform to Shannon entropy and thermodynamic kinetics of the test genome. Results are presented toward validation against available data. Pertinent details are reviewed in the context of their possible uses in rational vaccine designs.

Keywords: ssDNA; single-stranded DNA; viral genome; energetics; hairpin bending; codon-non-codon delineation; CpG island; vaccine design; viral DNA; bioinformatics; Shannon entropy; thermodynamic kinetics.

DOI: 10.1504/IJBRA.2011.041736

International Journal of Bioinformatics Research and Applications, 2011 Vol.7 No.3, pp.239 - 261

Published online: 02 Aug 2011 *

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