Automating intron landscaping for fungal mitochondrial genomes

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dc.contributor.authorPawliszak, Tanya
dc.contributor.examiningcommitteeLeung, Carson K. (Computer Science)
dc.contributor.examiningcommitteeHausner, Georg (Microbiology)
dc.contributor.supervisorTremblay-Savard, Olivier
dc.date.accessioned2025-01-13T22:21:11Z
dc.date.available2025-01-13T22:21:11Z
dc.date.issued2024-12-12
dc.date.submitted2024-12-12T21:28:45Zen_US
dc.date.submitted2025-01-07T18:31:04Zen_US
dc.date.submitted2025-01-13T21:55:09Zen_US
dc.degree.disciplineComputer Science
dc.degree.levelMaster of Science (M.Sc.)
dc.description.abstractIntron landscapes in mitochondrial genomes play a crucial role in the regulation of gene expression and overall mitochondrial function. However, the complexity and variability of intron structures across different fungal species present significant challenges for manual annotation and analysis. This thesis presents an automated approach for intron landscaping in fungal mitochondrial genomes, leveraging advanced computational tools to streamline the identification, characterization, and classification of introns. By integrating a combination of computational tools that are used in different areas of the identification of Group I Introns, my pipeline, HMMER Infernal Pipeline (or HIPipeline), enhances the accuracy and efficiency of intron detection, significantly reducing the need for labor-intensive manual curation. Indeed, our results on 25 mitochondrial genomes of fungi has shown high levels of sensitivity and precision for the positions of the introns. We validate the approach using a diverse set of fungal mitochondrial genomes, demonstrating its robustness in capturing intron subtype identification and positions. This automation not only accelerates the annotation process but can also facilitate comparative genomic studies and functional analyses of mitochondrial introns across different fungal species.
dc.description.noteFebruary 2025
dc.identifier.urihttp://hdl.handle.net/1993/38794
dc.language.isoeng
dc.subjectGroup I Introns
dc.subjectIntron
dc.subjectIntron landscapes
dc.subjectHMMER
dc.subjectInfernal
dc.subjectfungal
dc.subjectgenomes
dc.subjectmitochondrial
dc.subjectIntron mapping
dc.subjectIntron landscaping
dc.titleAutomating intron landscaping for fungal mitochondrial genomes
local.subject.manitobano
oaire.awardNumberRGPIN-2016-06051
oaire.awardTitleAnalysis of tRNA gene evolution in bacterial genomes
oaire.awardURIhttps://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=749933
project.funder.identifierhttps://doi.org/10.13039/501100000038
project.funder.nameNatural Sciences and Engineering Research Council of Canada
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