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ReciMap: a pipeline to identify rearrangement borders between closely related genomes
Thesis (MSc)--Stellenbosch University, 2024.
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| Format: | Thesis |
| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2024
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| _version_ | 1867613876976091136 |
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| access_status_str | Open Access |
| author | Schutte, Casper Jan Hendrik |
| author2 | Patterton, Hugh-George |
| author_browse | Patterton, Hugh-George Schutte, Casper Jan Hendrik |
| author_facet | Patterton, Hugh-George Schutte, Casper Jan Hendrik |
| author_sort | Schutte, Casper Jan Hendrik |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MSc)--Stellenbosch University, 2024. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/130331 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:43:06.958Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/130331 ReciMap: a pipeline to identify rearrangement borders between closely related genomes Schutte, Casper Jan Hendrik Patterton, Hugh-George Stellenbosch University. Faculty of Medicine and Health Sciences. Centre for Bioinformatics & Computational Biology. Bioinformatics Evolutionary genetics -- Data processing Genomics Computational biology UCTD Thesis (MSc)--Stellenbosch University, 2024. 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. AFRIKAANSE OPSOMMING: Grootskaalse genomiese herrangskikking speel ’n sleutel rol in die evolusie van genome en in spesiasie. Gegewe die duidelike noodsaaklikheid vir ’n robuuste instrument, stel hierdie tesis ReciMap bekend, ’n terminaal–gebasseerde bioinformatika program wat geskep is om die grense van genomiese herskikkings tussen naby–verwante genome akkuraat te identifiseer. Die program maak gebruik van die wederkerige passing van kort, sintetiese sekwensies. Die ontwikkeling van ReciMap word breedvoerig beskryf in hierdie tesis. Ons demonstreer die program se doeltreffendheid om die grense van herrangskikkings akkuraat aan te dui met ’n resolusie van ongeveer 4 basispare. Ten einde die program se akkuraatheid te verifieer, voer ons deeglike vergelykings uit met genome wat toenemend evolusionˆer divergeer, met tot vyftig duisend generasie verskille. Die veelsydigheid van ReciMap demonstreer sy vermo¨e om nuwe metodes vir die identi- fikasie van sintenie blokke in te sluit. Hierdie eienskap vergroot die bruikbaarheid van die program en maak ’n meer omvattende ontleding van genoom argitektuur moont- lik. ReciMap word beskikbaar gestel as ’n oop–bron, terminaal–gebaseerde instrument wat toeganklik is vir navorsers. ReciMap is openbaar beskikbaar by die volgende URL: https://github.com/casper-schutte/recimap. Hierdie navorsing dra nie net ’n waardevolle berekenings hulpbron by tot die veld van bioinformatika nie, maar bied ook ’n nuwe benadering tot die identifikasie van grense in genomiese herrangskikkings. Masters 2024-02-29T15:58:10Z 2024-04-26T13:43:12Z 2024-02-29T15:58:10Z 2024-04-26T13:43:12Z 2024-03 Thesis https://scholar.sun.ac.za/handle/10019.1/130331 en_ZA Stellenbosch University application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Bioinformatics Evolutionary genetics -- Data processing Genomics Computational biology UCTD Schutte, Casper Jan Hendrik ReciMap: a pipeline to identify rearrangement borders between closely related genomes |
| title | ReciMap: a pipeline to identify rearrangement borders between closely related genomes |
| title_full | ReciMap: a pipeline to identify rearrangement borders between closely related genomes |
| title_fullStr | ReciMap: a pipeline to identify rearrangement borders between closely related genomes |
| title_full_unstemmed | ReciMap: a pipeline to identify rearrangement borders between closely related genomes |
| title_short | ReciMap: a pipeline to identify rearrangement borders between closely related genomes |
| title_sort | recimap a pipeline to identify rearrangement borders between closely related genomes |
| topic | Bioinformatics Evolutionary genetics -- Data processing Genomics Computational biology UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/130331 |
| work_keys_str_mv | AT schuttecasperjanhendrik recimapapipelinetoidentifyrearrangementbordersbetweencloselyrelatedgenomes |