Fast analysis of genomic homologies: Primate immunodeficiency virus |
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Authors: | Maurice L J Moncany Pascal R R Courtois |
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Institution: | (1) Laboratory of Cellular and Molecular Biology, University of La Rochelle, Avenue Marillac, 17042 La Rochelle Cedex 1, France;(2) Computer Science Laboratory, Conservatoire National des Arts et Métiers (CNAM), 292 rue Saint-Martin, 75003 Paris, France |
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Abstract: | We have recently published a new probabilistic algorithm which performs genomic comparisons on a huge scale. In the present
paper it was applied to immunodeficiency viral sequences extracted from international gene databanks. During global sequence
analysis of human (HIV I and HIV2) and simian viruses by means of dot-matrix representation, series of homology were obtained
which permitted the definition of families of viruses overlapping the species divisions. Sequences of interest were characterized
to the lexical base sentence through successive zoomings. Strain-to-strain comparison confirmed subfamily classifications
and led, for example, to the identification of divergent LTR sequences. By way of example, we described the application of
the algorithm to the ANT70C and MVP5180 HIV1-O viruses, for which the observed differences were shown to correspond to a deletion
in the U3 region, situated between the LEF and NF-κB sites. It was of interest to consider these data in a tentative phylogenetic
interpretation.
Correspondence to: M.L.J. Moncany |
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Keywords: | Primate immunodeficiency virus Genomic analysis Genome comparison HIV1 HIV2 SIV Probabilistic algorithm Phylogenetic analysis |
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