Implement an R package for miRNA gene finding

Status: Closed

Thesis: Bachelor

Field: Genomics, NGS, Programming

Advisors:  Evers, Engelmann

Courses Required:  Practical Bioinformatics II

Objective: We have developed a pipeline to detect miRNA precursors from RNA sequencing reads. To improve usability, the pipeline should run in R (and invoke scripts outside of R), or alternatively another programming language that the student knows well. The pipeline should be extended with graphical output and summarize results in a format that is easily understood by users.

First-Steps: Get familiar with miRNA gene finding in general, and our miRNA gene finding pipeline in particular.

Start Reading:

"Current tools for the identification of miRNA genes and their targets" (2009) Mendes et al. www.ncbi.nlm.nih.gov/pmc/articles/PMC2677885/

"Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role" (2013) Kleftogiannis et al.  http://www.sciencedirect.com/science/article/pii/S1532046413000221