Accelerator  for DNA Sequence Alignment

One of the most popular operations in personalized medicine is protein or DNA sequence database search based on pair-wise alignment, where a query sequence is compared with a database of sequences to find a highest-similarity sequence. This similarity can provide insights on the functionality of the query protein or the role of a gene. Conventional computer architecture is proven to be inefficient for personalized medicine tasks. For example, aligning even several hundred DNA or protein sequences consumes several CPU hours on high performance computer. Hence, personalized medicine relies on hardware accelerators to keep up with the increasing amount of data generated from biology applications.

In this project, we will design a stand-alone accelerator for sequence alignment for personalized medicine applications.

This is a research project, endeavoring into a new field of study, which may lead to further research and scientific publications.
What will we do and learn in the project?
1. Learn digital VLSI design tools and flow
2. Design a novel accelerator for machine learning

• Logic design course
• Desire to innovate and try new things
• Ability to work independently

Prerequisites:  Digital Systems and Computer Structure – 044252