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

BMC Research Notes

Joe Francoeur¹  Andrzej K Brodzik¹ 

[1] The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA

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

Others  :  1167583
DOI  :  10.1186/1756-0500-4-114

 received in 2010-12-10, accepted in 2011-04-08,  发布年份 2011

【 摘 要 】

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In this work three strains of the Bacillus anthracis genome are compared and previously unpublished single nucleotide polymorphisms (SNPs) are revealed.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.

【 授权许可】

   
2011 Brodzik et al; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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