Unsupervised statistical identification of genomic islands using oligonucleotide distributions with application to Vibrio genomes

Nag, Sanjay ; Chatterjee, Raghunath ; Chaudhuri, Keya ; Chaudhuri, Probal (2006) Unsupervised statistical identification of genomic islands using oligonucleotide distributions with application to Vibrio genomes Sadhana (Academy Proceedings in Engineering Sciences), 31 (2). pp. 105-115. ISSN 0256-2499

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Official URL: http://www.ias.ac.in/sadhana/Pdf2006Apr/105.pdf

Related URL: http://dx.doi.org/10.1007/BF02719776

Abstract

Vibrio cholerae, Vibrio vulnificus, Vibrio parahaemolyticus and several other related Vibrio species show distinctly similar two-chromosomal genome organization. However, the modes of pathogenicity are very different among these species, and this is largely attributed to externally acquired genetic elements. We develop some statistical methods to determine these external genetic elements or genomic islands in genomes based on their differential oligonucleotide usage patterns compared to the rest of the genome. Genomic islands identified by these unsupervised statistical methods include integron and pathogenicity islands. After statistical determination of the genomic islands, we investigate their gene contents and their possible association with the pathogenic behaviour of the corresponding Vibrio species. These investigations lead to observations that are of evolutionary and biological significance.

Item Type:Article
Source:Copyright of this article belongs to Indian Academy of Sciences.
Keywords:Dendrogram; Hierarchical Clustering; Horizontally Acquired Genes; Oligonucleotide Distributions; Statistical Test of Significance; Transposons
ID Code:8126
Deposited On:26 Oct 2010 04:19
Last Modified:16 May 2016 18:11

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