Ayesha Mahfuz L&S Math & Physical Sciences
AncestralClust: Designing Probes for Target DNA capture
My research project as a SURF fellow focuses on developing innovative DNA probes to enhance the capture of targeted genomic sequences. Utilizing our lab’s open-source tool, AncestralClust, I aim to refine and expand the design of probes that can accurately and efficiently target specific regions within genomes such as ITS2 and C01. The latter comprises over 2 million sequences, presenting a complex challenge in bioinformatics. By adjusting various parameters within AncestralClust, such as the number of sequence clusters and the minimum descendants per branch, I strive to optimize probe design to achieve maximal sequence coverage. Our goal is to be able to target as many organisms as possible by optimizing our target probe strategy, so that we can get a comprehensive and unbiased composition of the organisms that make up a sample.
Message To Sponsor
Thank you so much to Leadership for sponsoring my SURF project this summer! I not only had a unique, fun summer experience, but the entire SURF program was very educationally enriching, from my own research project to all the workshops and meetings that SURF hosted. I also got to learn about various other research projects, which really broadened my view of what research fields I might be interested in pursuing in the future. Thanks to Leadership and SURF, I was able to dedicate time to work on my project and discover results that I didn't think were possible when I first started pursuing this idea.