IIBR Informatics: Integrating codon evolution and sequence-assembly error models into multiple sequence alignment

Arizona State University, Scottsdale AZ

Investigators

Abstract

The information age has fundamentally changed the way most areas of science operate. Advances in genomics and informatics have radically reshaped the life sciences, producing innovations that impact multiple ares including medicine and agriculture. This project will design new computational methods and software to manage the complexities of modern genomic datasets, addressing challenges that existing approaches have overlooked. As computational training is essential for modern biology students, this project will broaden the participation in computing by training faculty and instructors at regional, community, and tribal colleges in evidence-based practices for teaching computing skills to students. This project will develop new computational methods to analyze genetic data using statistical models that are optimized for the challenges of modern datasets. First, new finite-state transducer models will be developed for aligning genetic and genomic sequences that capture the biological and technical process that shape modern datasets. Second, these models will be implemented in COATi, a new multiple-sequence alignment tool that will be free and open-sourced. Thirdly, COATi will be used to understand understudied features of molecular evolution. In addition, Software Carpentry Instructor training workshops will be held for faculty at regional, community, and tribal colleges, which will improve the quality of computational instruction at these institutions, and thus broaden the participation in computing for students from underrepresented and underserved backgrounds. The results of the project are available at https://cartwrig.ht/coati/. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.