Title: Geometric global genomic informatics for RNA viruses

Authors: Douglas J. Cork, Dachywan Wu, Michael J. North

Addresses: Department of Biological, Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA. ' Department of Biological, Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA. ' Center for Complex Adaptive Agent Systems Simulation, Argonne National Laboratory, Decision and Information Sciences Division, 9700 S. Cass Avenue, Argonne, IL 60439-4867 USA; Computation Institute, University of Chicago, Chicago, IL 60637 USA

Abstract: The W-curve is in the class of autoregressive, geometrical algorithms that will permit bioinformaticists to visualise repeating and/or shifting patterns embedded within the whole genome. Herein, we inspect whole HIV-1 genomes. Conventional string based phylogenetic trees are insufficient to visualise the 3-D information content of an HIV-1 genome. String based analysis cannot visualise, as can a typical W-curve based treatment, the subtlety of quasi-species shifting between different HIV-1 genomes. Herein we have conveyed some of the similar patterns embedded in different HIV-1 genomes. It is hoped that conventional string-based phylogenetic trees will enjoy some reinterpretation of the definition of quasi-species of the HIV-1 genome, in light of HIV-1 shift experiment performed with W-curves.

Keywords: genetic sequence visualisation; HIV-1 genomes; W-curves; autoregressive algorithms; geometric global genomics; genomic information content; RNA viruses; global genomic informatics; bioinformatics.

DOI: 10.1504/IJMEI.2008.020752

International Journal of Medical Engineering and Informatics, 2008 Vol.1 No.2, pp.227 - 249

Published online: 13 Oct 2008 *

Full-text access for editors Full-text access for subscribers Purchase this article Comment on this article