Masters Degrees (Centre for Bioinformatics & Computational Biology)

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Browsing Masters Degrees (Centre for Bioinformatics & Computational Biology) by Subject "Computational biology"

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    ReciMap: a pipeline to identify rearrangement borders between closely related genomes
    (Stellenbosch : Stellenbosch University, 2024-03) Schutte, Casper Jan Hendrik; Patterton, Hugh-George; Stellenbosch University. Faculty of Medicine and Health Sciences. Centre for Bioinformatics & Computational Biology.
    ENGLISH ABSTRACT: Large genomic rearrangement events play a pivotal role in the evolutionary dynamics of genomes and the process of speciation. Recognizing the necessity for a robust tool, this thesis introduces ReciMap, a command line bioinformatics pipeline explicitly created to precisely identify the borders of genomic rearrangement events between closely related genomes. The pipeline leverages the reciprocal mapping of short, synthetic reads as a methodological approach. The development of ReciMap is extensively detailed in this thesis. We demonstrate the pipeline’s efficacy in accurately pinpointing the borders of rearrangement events with a resolution of approximately 4 base pairs (bp). To validate the pipeline’s accuracy, we conduct thorough comparisons of genomes with increasing evolutionary divergence, up to fifty thousand generations apart. Moreover, the versatility of ReciMap is showcased in its capability to incorporate novel methods for the identification of synteny blocks. This feature broadens the utility of the pipeline, allowing for a more comprehensive analysis of genomic architecture. ReciMap is introduced as an open–source, command line–based tool, accessible to researchers and practitioners alike. The repository for ReciMap is publicly available at the following URL: https://github.com/casper-schutte/recimap This research not only contributes a valuable computational resource to the field of bioinformatics but also presents a novel approach to border identification in genomic rearrangement events.