The Development of Computational Methods for Studying Plant-Pathogen Interactions Public

http://ir.library.oregonstate.edu/concern/honors_college_theses/br86b549q

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  • Modern technology has enabled the advancement of biological research through the use of powerful machines and computers as well as innovative computer programs. Advances in sequencing technology and software enable us to make de novo assemblies of organism genomes, and the development of specialized computer programs can automate routine but tedious tasks that are done by hand. We are studying plant-bacteria interactions. The immune response of a plant to a pathogen can be quantified by counting callose spots in pictures of leaves. The need for an objective and fast method to count these spots led to the development of AutoSPOTs. This computer program, written in Perl, identifies and counts spots in images based on spot color and size, and includes features that previous spot-counting software did not have. AutoSPOTs has user-configured filters that can be used to both include and exclude different types of spots from being counted. We have also de novo assembled a draft genome of the plant pathogen Rhodococcus fascians. This draft genome has been assembled from both mate-pair and paired-end reads. I wrote a set of scripts to filter out poor-quality reads from the dataset in order to improve the quality of our assembly. We are confident in our assembly due to the presence of a contig that is a potential match for R. fascian’s linear plasmid, as well as its consistency when assembled from different sets of reads.
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