GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequenci

Background: Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis is thus essential to our understanding of how selective and neutral forces shape bacterial populations over a short period of time. The Solexa Genome Analyzer, a next-generation sequencing platform, allows millions of short sequencing reads to be obtained with great accuracy, allowing for the ability to study the dynamics of the bacterial population at the whole genome level. The tool referred to as GenHtr was developed for genome-wide heterogeneity analysis. Results: For particular bacterial strains, GenHtr relies on a set of Solexa short reads on given bacteria pathogens and their isogenic reference genome to identify heterogeneity sites, the chromosomal positions wit...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: GongXin Yu
• Keywords: Bacterial Population, BMCBI 2010, Genome-wide Heterogeneity, Heterogeneity Analysis