NDLI: Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition

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Molecular BioSystems Vol - 5 Issue - 9

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Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition

Content Provider	Royal Society of Chemistry (RSC)
Author	Rangannan, Vetriselvi Bansal, Manju
Copyright Year	2009
Abstract	The rapid increase in genome sequence information has necessitated the annotation of their functional elements, particularly those occurring in the non-coding regions, in the genomic context. Promoter region is the key regulatory region, which enables the gene to be transcribed or repressed, but it is difficult to determine experimentally. Hence an in silico identification of promoters is crucial in order to guide experimental work and to pin point the key region that controls the transcription initiation of a gene. In this analysis, we demonstrate that while the promoter regions are in general less stable than the flanking regions, their average free energy varies depending on the GC composition of the flanking genomic sequence. We have therefore obtained a set of free energy threshold values, for genomic DNA with varying GC content and used them as generic criteria for predicting promoter regions in several microbial genomes, using an in-house developed tool ‘PromPredict’. On applying it to predict promoter regions corresponding to the 1144 and 612 experimentally validated TSSs in E. coli (50.8% GC) and B. subtilis (43.5% GC) sensitivity of 99% and 95% and precision values of 58% and 60%, respectively, were achieved. For the limited data set of 81 TSSs available for M. tuberculosis (65.6% GC) a sensitivity of 100% and precision of 49% was obtained.
Starting Page	1758
Ending Page	1769
Page Count	12
File Format	HTM / HTML PDF
ISSN	1742206X
Volume Number	5
Issue Number	12
Journal	Molecular BioSystems
DOI	10.1039/b906535k
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	Gene Mycobacterium tuberculosis Pin Point, Georgia DNA Escherichia coli GC-content Genome Thermodynamic free energy
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biotechnology

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Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition.

Relative Stability Of DNA As A Generic Criterion For Promoter Prediction: Whole Genome Annotation Of Microbial Genomes With Varying Nucleotide Base Composition

Distinct frequency-distributions of homopolymeric DNA tracts in different genomes (1998)

Amelioration of bacterial genomes: rates of change and exchange (1997)

REFERENCES CONTENT ALERTS Whole-Genome Comparison of Mycobacterium tuberculosis Clinical and (2002)

The GC Content of Primates and Rodents Genomes Is Not at Equilibrium: A Reply to Antezana

Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes

Comparative Genomics of Escherichia coli Serotype O55:H7 Using Complete Closed Genomes

Escherichia coli and mycobacterium tuberculosis.

Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition

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Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition.

Relative Stability Of DNA As A Generic Criterion For Promoter Prediction: Whole Genome Annotation Of Microbial Genomes With Varying Nucleotide Base Composition

Distinct frequency-distributions of homopolymeric DNA tracts in different genomes (1998)

Amelioration of bacterial genomes: rates of change and exchange (1997)

REFERENCES CONTENT ALERTS Whole-Genome Comparison of Mycobacterium tuberculosis Clinical and (2002)

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Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes

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Escherichia coli and mycobacterium tuberculosis.

Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition