Projects and Internships
Bioinformatics Profile Students are expected to at least “do” a bioinformatics project (18EC) however we recommend to go for a 33EC (6 months) internship. On this page we try to list projects that are available trough our community. Of course you are always welcome to find your own group to do an internship (or project). Keep in mind to always discuss with your masters coordinator (tutor) to see if this bioinformatics internship (or project) also fits the requirements of your master.
Bioinformatic re-assembly of highly polymorphic plant resistance gene clusters
Plant resistance genes encode for receptors that recognize pathogen molecules and trigger an effective immune response. In plant genomes resistance genes are often clustered and highly polymorphic between lines of the same species. This means that the number and DNA sequences of resistance genes is highly variable making it impossible to easily compare these regions between lines. We are now using targeted locus amplication (TLA) followed by NGS to collect sequence reads of these regions. The challenge now is to assembly these reads into correct gene clusters. For this project you will start with Illumina reads of TLA samples and a reference genome. As simple mapping of reads to the reference will not work you will need to make a hybrid approach between mapping and de novo assembly followed by annotation. A method for this does not exist yet, so needs to be develop in the proposed project. A challenging and interesting project that is closely linked to the lab research of our Plant-Microbe Interactions group
- Posted on: November 17th – 2016
- Contact: email@example.com
- UBC Community: Ackerveken Group