Jen: Using Geneious to analyze DNA sequencing results
Hi, I'm Jen. I'm studying the alternative splicing of a gene involved in myelin formation. One tool I use is a mini-gene plasmid which contains several introns and exons of my favorite gene. I make mutations in this mini-gene plasmid, and after transfection and RNA isolation, I compare the amount of each alternative mRNA form made from the mutant construct to a normal one. Sometimes the mutations I make are randomly introduced with an error prone PCR, sometimes they are large deletions or insertions, and I also can re-create patient's mutations in this system using site directed mutagenesis.
Each of these plasmid mutation techniques requires a lot of plasmid screening. Sometimes I can use a restriction digest to determine if the mutation is there, and then I'm using sequencing just to confirm the change. But sequencing is the only way to screen my plasmids for random mutagenesis changes, and often the same is true for targeted mutagenesis.
Geneious has been a very useful tool to help me analyze my sequencing results, and I have been using Geneious since October 2006. I found it while searching online for usable freeware programs, and I noticed that it was an Apple Math and Science top download. I work in a academic/non-profit with a limited budget, so being able to use a program that does the basics (import, align and print) even when it is the free version, is very important to me and to the students I supervise. It does a great job with alignments, even when there are large deletions or insertions which can make other programs throw up their hands in confusion.
When using the Pro version, I enjoy the ability to view my chromatograms with the alignment. When the sequencing result gives a mixed base, like R Y M or K, using the full version allows me to see quickly if the R is really a small G peak between two strong 2 A peaks, or a mixed batch of G and A. Being able to print out the alignment and chromatogram and save it in my lab notebook is great.
When I'm not doing research, I'm quite busy at home with my husband and young daughter. My daughter occasionally lets me do hobby stuff like quilting and decorative painting, and she has recently come to enjoy gardening and rides in a bicycle pulled trailer, which are activities we can all enjoy together. Eventually I'd like to have a teaching position at a small college, and continue to supervise students doing undergraduate research.
Jen, Ph.D.
Delaware, USA