Gene order alignment on a phylogeny with BOPAL 2.0

Simple item page
dc.contributor.authorChua, Meghan
dc.contributor.examiningcommitteeTurgeon, Max (Computer Science/Statistics)en_US
dc.contributor.examiningcommitteeHausner, Georg (Microbiology)en_US
dc.contributor.supervisorTremblay-Savard, Olivier (Computer Science)en_US
dc.date.accessioned2022-02-02T20:32:08Z
dc.date.available2022-02-02T20:32:08Z
dc.date.copyright2022-02-02
dc.date.issued2021en_US
dc.date.submitted2022-02-02T19:03:32Zen_US
dc.degree.disciplineComputer Scienceen_US
dc.degree.levelMaster of Science (M.Sc.)en_US
dc.description.abstractTransfer RNA (tRNA) and ribosomal RNA (rRNA) genes are essential for the translation of messenger RNA (mRNA) into proteins. Studying how these genes evolve within a bacterial genus can reveal core sets of tRNA/rRNA genes and how these trends affect codon usage. The following research builds upon a previous algorithm called BOPAL which utilized operon information to better infer orthologous genes. The following research modifies BOPAL to properly handle singleton genes, adds a second pass to utilize previously inferred ancestors, and simplifies the backtracking algorithm by introducing a triple-wise alignment with a neighboring genome. These changes have culminated in a higher level of accuracy for the inferred events and ancestors compared to BOPAL. In our analysis, we also applied BOPAL 2.0 to a complex dataset of Clostridium genomes. Our results have found higher average rates of duplications, deletions, transpositions and substitution events in Clostridium than Bacillus but fewer inversions.en_US
dc.description.noteFebruary 2022en_US
dc.identifier.citationChua, Meghan, Anthony Tan, and Olivier Tremblay-Savard. "BOPAL 2.0 and a study of tRNA and rRNA gene evolution in Clostridium." Journal of Bioinformatics and Computational Biology (2021): 2140007.en_US
dc.identifier.urihttp://hdl.handle.net/1993/36255
dc.language.isoengen_US
dc.rightsopen accessen_US
dc.subjecttRNAen_US
dc.subjectrRNAen_US
dc.subjectAlgorithmen_US
dc.subjectInferenceen_US
dc.subjectEvolutionen_US
dc.subjectClostridiumen_US
dc.titleGene order alignment on a phylogeny with BOPAL 2.0en_US
dc.typemaster thesisen_US
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
chua_meghan.pdf
Size:
5.01 MB
Format:
Adobe Portable Document Format
Description:
Download
License bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
license.txt
Size:
2.2 KB
Format:
Item-specific license agreed to upon submission
Description:
Download
Collections
FGS - Electronic Theses and Practica