Assefaw Gebremedhin, Research, Bioinformatics

Management and Analysis of Short-Sequence Repeat Data

Patterns of short sequence repeats (SSRs) at a given loci are commonly used to identify different strains of a microorganism. In a new project we just began in collaboration with Prof. Kelly Brayton of the Allen School for Global Animal Health at WSU, my graduate student Helen Catanese and I are developing a robust software tool, called ReapeatAnalyzer, aimed at the management and analysis of SSR data on bacterial strains infecting cattle. Current functionalities of RepaeateAnalyzer include storing, managing, searching and identifying (i) repeats, (ii) the known strains that contain the repeats and (iii) the publication sources in which the findings are reported. A prototype of the tool is currently being used in tracking strains of A. Marginale in South Africa, the US and other places in the world. The tool however is being designed to be sufficiently flexible to be applied to any species with strains identified in terms of SSRs.

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