Jeffrey Grover - Homework 3

Codeacademy:

Finished! Things got a little rough near the end, but nothing insurmountable.

Rosalind:

You can see my code for exercise #2 here:

https://github.com/groverj3/PLS599/blob/master/Rosalind_INI2.py

Semester Project

I have changed my mind on my semester project. Instead, I will be working with published Arabidopsis thaliana methylome data and comparing DNA methylation profiles in different mutant backgrounds and tissues (dependent on data availability):

Contrary to our common understanding of DNA methylation in Arabidopsis, there are loci which have increased methylation when RdDM components are absent. I want to look in different mutant backgrounds and tissues for these regions.

For someone new to bioinformatics like me I think the most difficult part of this project will be identifying the differentially methylated regions and finding the regions with increased methylation, as opposed to decreased methylation. Mostly due to my limited experience working with sequence data. I think there should be ways to do this in python. If I'm able to get everything working correctly then I could also BLAST the hypermethylated regions to determine if they have anything in common functionally.

Working with bisulfite sequencing data would be beneficial since my own work may lead to doing that eventually.

References:

Mosher RA, Schwach F, Studholme D, Baulcombe DC. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci USA. 2008;105(8):3145-50.