Todd: Using Geneious in protein structure studies
My name Is Todd and I've been working on structure function studies of the Amyloid Precursor Protein (APP) at Yale. I found Geneious on Apple's software downloads page as well as a few other OSX sequencing packages. After trying them all out I decided to go with Geneious.
There are actually three APPs in higher eukaryotes (APP, APLP1, APLP2). I work on the C. elegans homologue of APP, since C. elegans has only one. We look for promising areas in the protein, make mutations and see what they do to the biochemical properties of the protein. If it looks interesting we look at what it does in the worm. As a result I make a lot of mutants.
I use Geneious to design my primers and to look at the mutagenesis sequence data to make sure we have the right mutant. First off, I like that Geneious runs on Mac under OSX and I really like the price. The Pro version allows me to quickly get the reading frame translated then aligned with the template and the wild type sequence. Another feature I really like is the chromatogram view. The sequence runs we do often have a few Ns in them. I can load all the files from a run (sequence and chromatogram) into Geneious then go through and manually assign the Ns.
I also like that Geneious can work with structure files as I can see exactly where my mutation will occur in the protein and what local residues it will interact with. This is a much better way to go about it that looking at the sequence alone.
I'll be starting a research faculty position soon at University of Maryland and I plan on using Geneious for all my mutagenesis work.
Todd