Geometric global genomic informatics for RNA viruses
by Douglas J. Cork, Dachywan Wu, Michael J. North
International Journal of Medical Engineering and Informatics (IJMEI), Vol. 1, No. 2, 2008

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.

Online publication date: Mon, 13-Oct-2008

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