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, we are developing a robust software tool, called RepeatAnalyzer, aimed at the management and analysis of SSR data on bacterial strains infecting cattle. Currently RepeatAnalyzer contains a dataset on the bacteria A. marginale, and the tool’s functionalities 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, Asia and different groups in the US. The tool however is being designed to be sufficiently flexible to be applied to any species with strains identified in terms of SSRs.

Papers

  • H. Catanese, K. Brayton and A.H. Gebremedhin. A Nearest-Neighbors Network Model for Sequence Data Reveals New Insight into Genotype Distribution of a Pathogen, BMC Bioinformatics (2018) 19:475. https://doi.org/10.1186/s12859-018-2453-2.
    Abstract    Paper in PDF
  • H.N. Catanese, K.A. Brayton and A.H. Gebremedhin, RepeatAnalyzer: a tool for analysing and managing short-sequence repeat data, BMC Genomics 2016 17:422. DOI: 10.1186/s12864-016-2686-2
    Abstract    Paper in HTML
  • Z.T.H. Khumalo, H.N. Catanese, N. Leisching, P. Hove, N.E. Collins, M.E. Chaisit,  A.H. Gebremedhin, M.C. Oosthuizen and K.A. Brayton, Characterization of Anaplasma marginale subspecies centrale using msp1aS genotyping reveals wildfire reservoir,  Journal of Clinical Microbiology, 2016 54:10, 2503-2512
    Abstract    Paper in HTML
  • P. Hove, M.E. Chaisi, K.A. Brayton, H. Ganesan, H.N. Catanese, M.S. Mtshali, A.M. Mutshembele, M.C. Oosthuizen, and N.E. Collins, Co-infections with multiple genotypes of Anaplasma marginale in cattle indicate pathogen diversity, Parasites & Vectors (In press)
    Abstract
  • Z.T.H. Khumalo, H.N. Catanese, N. Leisching, P. Hove, N.E. Collins, M.E. Chaisit, A.H. Gebremedhin, M.C. Oosthuizen and K.A. Brayton, Characterization of Anaplasma marginale subspecies centrale using msp1aS genotyping reveals wildfire reservoir, Journal of Clinical Microbiology 2016 54:10, 2503-2512.