Undergraduate (Physiology major)
dugger@email.arizona.edu
Ph. 520 626 1727
Office: BSW121
I use bioinformatic approaches to measure how aggregation-prone different polypeptide sequences are. I then look for evidence of how this acts as an evolutionary constraint at the sequence level. Using the Perl programming language along with BioPerl, I have written several scripts for analyzing aggregation tendency in relation to expression level. I hope to expand some of my scripts and write a Perl interface for TANGO (a tool which predicts the likelihood that a peptide sequence is to aggregate). I would also like to write several Perl modules to allow the large scale data analysis, such as streamlining a method for TANGO analysis.
Tools I use:
- BioPerl: This is a very useful package for bioinformatics, if you’re using Perl and looking to do anything involving biology then you need this. It’s fairly well documented, with several quick-start as well as in-depth tutorials.
- Perl: The programming language I use. Very good for our purposes, flexible and great libraries to do almost anything. Plus it’s fairly quick. Active Perl is a version of Perl suitable for Win32 systems. Perl is bundled by default on most Linux distributions
- TANGO, a statistical algorithm that predicts how likely a peptide sequence is to aggregate, that is, unfold itself into an undesired peptide sequence.