Sequence Alignment - Hidden Markov Models, Category Theory and All That Jazz by Soumyashant Nayak

Explore the history and evolution of sequence alignment in this comprehensive colloquium talk. Delve into the fundamentals of RNA-Seq technology and its applications in biomedical research. Learn about key algorithms like BLAST, Needleman-Wunsch, and Smith-Waterman, as well as modern pseudo-alignment methods for transcript-level quantification. Discover the connections between sequence alignment and evolutionary genetics, and gain insights into hidden Markov models and their role in bioinformatics. The speaker also touches on the emerging field of applied category theory in organizing ideas within this domain. Engage with a detailed exploration of topics including central dogma, mutations, global vs. local alignment, and multiple sequence alignment, concluding with a Q&A session.

Date: Tue, 20 August 2019, 15:00 to
Sequence Aligment: Hidden Markov Models, Category Theory and all that jazz
An Overview of Sequence Alignment
Central Dogma
Sequences of Interest
exon Exon
Mutations Sequence Alterations
What is Sequence Alignment?
Why care about sequence alignment?
Pairwise Sequence Alignment
Global Alignment vs. Local Alignment
Needleman-Wunsch Algorithm 1970
Smith-Waterman algorithm 1981
Pseudo-alignment for quantification
Remarks on accuracy of kallisto
Idealized coverage & Realistic coverage
Blast
Hidden Markov Models
Multiple Sequence Alignment
The Main Problem
Next Steps
Acknowledgments
Thank You!
Q&A