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

Brodzik AK, Francoeur J - BMC Res Notes (2011)

Bottom Line: In this work three strains of the Bacillus anthracis genome are compared and previously unpublished single nucleotide polymorphisms (SNPs) are revealed.Moreover, it is shown that, despite the highly monomorphic nature of Bacillus anthracis, the SNPs are (1)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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA. abrodzik@mitre.org.

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Findings: In this work three strains of the Bacillus anthracis genome are compared and previously unpublished single nucleotide polymorphisms (SNPs) are revealed.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

No MeSH data available.


Related in: MedlinePlus

Histogram of distances between subsequent SNPs in the B. anthracis chromosome. The minimum, average and maximum distance between subsequent SNPs is 2, 34499 and 163349 bp, respectively, however many SNPs are less than 2000 bp apart.
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Figure 3: Histogram of distances between subsequent SNPs in the B. anthracis chromosome. The minimum, average and maximum distance between subsequent SNPs is 2, 34499 and 163349 bp, respectively, however many SNPs are less than 2000 bp apart.

Mentions: The results of the SNP analysis of the B. anthracis genome are summarized in Tables 1 and 2. The distributions of the chromosomal SNPs (all and non-synonymous) are shown in Figures 1 and 2. The histogram of distances between subsequent chromosomal SNPs is shown in Figure 3. A list of all SNPs annotated for position, nucleotide letter, coincidence with a coding region, and protein preservation is included in [Additional file 1].


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

Brodzik AK, Francoeur J - BMC Res Notes (2011)

Histogram of distances between subsequent SNPs in the B. anthracis chromosome. The minimum, average and maximum distance between subsequent SNPs is 2, 34499 and 163349 bp, respectively, however many SNPs are less than 2000 bp apart.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3094368&req=5

Figure 3: Histogram of distances between subsequent SNPs in the B. anthracis chromosome. The minimum, average and maximum distance between subsequent SNPs is 2, 34499 and 163349 bp, respectively, however many SNPs are less than 2000 bp apart.
Mentions: The results of the SNP analysis of the B. anthracis genome are summarized in Tables 1 and 2. The distributions of the chromosomal SNPs (all and non-synonymous) are shown in Figures 1 and 2. The histogram of distances between subsequent chromosomal SNPs is shown in Figure 3. A list of all SNPs annotated for position, nucleotide letter, coincidence with a coding region, and protein preservation is included in [Additional file 1].

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: The MITRE Corporation, 202 Burlington Road, Bedford, MA 01730, USA. abrodzik@mitre.org.

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.

No MeSH data available.


Related in: MedlinePlus