On detection and Assessment of Statistical Significance of Genomic Islands
IR@IICB: CSIR-Indian Institute of Chemical Biology, Kolkata
View Archive Info| Field | Value | |
| Title |
On detection and Assessment of Statistical Significance of Genomic Islands
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| Creator |
Chatterjee, Raghunath
Chaudhuri, Keya Chaudhuri, Probal |
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| Subject |
Molecular & Human Genetics
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| Description |
Many of the available methods for detecting Genomic Islands (GIs) in prokaryotic
genomes use markers such as transposons, proximal tRNAs, flanking repeats etc., or they use other
supervised techniques requiring training datasets. Most of these methods are primarily based on
the biases in GC content or codon and amino acid usage of the islands. However, these methods
either do not use any formal statistical test of significance or use statistical tests for which the
critical values and the P-values are not adequately justified. We propose a method, which is
unsupervised in nature and uses Monte-Carlo statistical tests based on randomly selected segments
of a chromosome. Such tests are supported by precise statistical distribution theory, and
consequently, the resulting P-values are quite reliable for making the decision.
Our algorithm (named Design-Island, an acronym for Detection of Statistically Significant
Genomic Island) runs in two phases. Some 'putative GIs' are identified in the first phase, and those
are refined into smaller segments containing horizontally acquired genes in the refinement phase.
This method is applied to Salmonella typhi CT18 genome leading to the discovery of several new
pathogenicity, antibiotic resistance and metabolic islands that were missed by earlier methods.
Many of these islands contain mobile genetic elements like phage-mediated genes, transposons,
integrase and IS elements confirming their horizontal acquirement.
The proposed method is based on statistical tests supported by precise distribution
theory and reliable P-values along with a technique for visualizing statistically significant islands. The
performance of our method is better than many other well known methods in terms of their
sensitivity and accuracy, and in terms of specificity, it is comparable to other methods.
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| Date |
2008
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| Type |
Article
PeerReviewed |
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| Format |
application/pdf
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| Identifier |
http://www.eprints.iicb.res.in/299/1/BMC_GENOMICS%2C_9(_150)%2C2008[100].pdf
Chatterjee, Raghunath and Chaudhuri, Keya and Chaudhuri, Probal (2008) On detection and Assessment of Statistical Significance of Genomic Islands. BMC Genomics, 9 (150). 01-11. |
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| Relation |
http://dx.doi.org/10.1186/1471-2164-9-150
http://www.eprints.iicb.res.in/299/ |
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