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Open Access Short Report

A new approach to in silico SNP detection and some new SNPs in the Bacillus anthracis genome

Andrzej K Brodzik* and Joe Francoeur

Author Affiliations

The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA

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BMC Research Notes 2011, 4:114  doi:10.1186/1756-0500-4-114

Published: 8 April 2011

Abstract

Background

Bacillus anthracis is one of the most monomorphic pathogens known. Identification of polymorphisms in its genome is essential for taxonomic classification, for determination of recent evolutionary changes, and for evaluation of pathogenic potency.

Findings

In this work three strains of the Bacillus anthracis genome are compared and previously unpublished single nucleotide polymorphisms (SNPs) are revealed. Moreover, it is shown that, despite the highly monomorphic nature of Bacillus anthracis, the SNPs are (1) abundant in the genome and (2) distributed relatively uniformly across the sequence.

Conclusions

The findings support the proposition that SNPs, together with indels and variable number tandem repeats (VNTRs), can be used effectively not only for the differentiation of perfect strain data, but also for the comparison of moderately incomplete, noisy and, in some cases, unknown Bacillus anthracis strains. In the case when the data is of still lower quality, a new DNA sequence fingerprinting approach based on recently introduced markers, based on combinatorial-analytic concepts and called cyclic difference sets, can be used.

Keywords:
Bacillus anthracis; cyclic difference sets; DNA sequence homology assessment; DNA sequence markers; SNP; strain comparison