Alignment-free analyses of nucleic acid sequences using graphical representation (with special reference to pandemic bird flu and swine flu)

Ashesh Nandy, Antara De, Proyasha Roy, Munna Dutta, Moumita Roy, Dwaipayan Sen, Subhash C. Basak

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

The exponential growth in database of bio-molecular sequences have spawned many approaches towards storage, retrieval, classification and analyses requirements. Alignment-free techniques such as graphical representations and numerical characterisation (GRANCH) methods have enabled some detailed analyses of large sequences and found a number of different applications in the eukaryotic and prokaryotic domain. In particular, recalling the history of pandemic influenza in brief, we have followed the progress of viral infections such as bird flu of 1997 onwards and determined that the virus can spread conserved over space and time, that influenza virus can undergo fairly conspicuous recombination-like events in segmented genes, that certain segments of the neuraminidase and hemagglutinin surface proteins remain conserved and can be targeted for peptide vaccines. We recount in some detail a few of the representative GRANCH techniques to provide a glimpse of how these methods are used in formulating quantitative sequence descriptors to analyse DNA, RNA and protein sequences to derive meaningful results. Finally, we survey the surveillance techniques with a special reference to how the GRANCH techniques can be used for the purpose and recount the forecasts made of possible metamorphosis of pandemic bird flu to pandemic human infecting agents.

Original languageEnglish (US)
Title of host publicationSynthetic Biology
Subtitle of host publicationOmics Tools and Their Applications
PublisherSpringer Singapore
Pages142-188
Number of pages47
ISBN (Electronic)9789811086939
ISBN (Print)9789811086922
DOIs
StatePublished - Oct 1 2018

    Fingerprint

Keywords

  • 3D plot
  • Adjacency matrix
  • Alignment-free graphical representation methods
  • Antigenic drift
  • Antigenic shift
  • BLAST
  • Betaglobin sequences
  • DE/ DG matrix
  • DNA/RNA sequence
  • Distance matrix
  • Ethics in surveillance
  • Euclidean distance
  • Flu vaccines
  • Genes and genomic sequences
  • Graph invariant
  • Graph theory
  • Graph-theoretical (topological) distance
  • Graphical representation and numerical characterisation (GRANCH)
  • H1N1 flu virus
  • H5N1 avian flu
  • Hemagglutinin (HA)
  • L/L matrix
  • M/M matrix
  • Mathematical descriptors
  • Molecular sequence similarity/dissimilarity
  • Mutations through recombination
  • Negative-sense strand RNA virus
  • Neuraminidase (NA)
  • Numerical characterisations of DNA/RNA/protein sequences
  • Pandemics
  • Protein sequences
  • Sialic acid residue
  • Spanish influenza
  • Surveillance of flu

Cite this

Nandy, A., De, A., Roy, P., Dutta, M., Roy, M., Sen, D., & Basak, S. C. (2018). Alignment-free analyses of nucleic acid sequences using graphical representation (with special reference to pandemic bird flu and swine flu). In Synthetic Biology: Omics Tools and Their Applications (pp. 142-188). Springer Singapore. https://doi.org/10.1007/978-981-10-8693-9_9