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Publication year
2009Source
Bioinformatics, 25, 3, (2009), pp. 309-314ISSN
Publication type
Article / Letter to editor

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Organization
CMBI
Former Organization
Bioinformatics (umcn)
Journal title
Bioinformatics
Volume
vol. 25
Issue
iss. 3
Page start
p. 309
Page end
p. 314
Subject
NCMLS 4: Energy and redox metabolismAbstract
MOTIVATION: Pangenome arrays contain DNA oligomers targeting several sequenced reference genomes from the same species. In microbiology, these can be employed to investigate the often high genetic variability within a species by comparative genome hybridization (CGH). The biological interpretation of pangenome CGH data depends on the ability to compare strains at a functional level, particularly by comparing the presence or absence of orthologous genes. Due to the high genetic variability, available genotype-calling algorithms can not be applied to pangenome CGH data. RESULTS: We have developed the algorithm PanCGH that incorporates orthology information about genes to predict the presence or absence of orthologous genes in a query organism using CGH arrays that target the genomes of sequenced representatives of a group of microorganisms. PanCGH was tested and applied in the analysis of genetic diversity among 39 Lactococcus lactis strains from three different subspecies (lactis.cremoris, hordniae) and isolated from two different niches (dairy and plant). Clustering of these strains using the presence/absence data of gene orthologs revealed a clear separation between different subspecies and reflected the niche of the strains.
This item appears in the following Collection(s)
- Academic publications [202923]
- Electronic publications [101091]
- Faculty of Medical Sciences [80072]
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