Talks
Spring 2016

Fundamentals of Stringology I: Recap on Exact Pattern Matching and Alignment Algorithms

Tuesday, January 19th, 2016 9:30 am10:30 am

Add to Calendar

Speaker: 

Dan Gusfield (UC Davis)

The purpose of these lectures is to give a quick, but rigorous introduction to the most fundamental and general algorithmic techniques that arise in biological  sequence analysis, and to review open problems in the probability of sequence alignment. Some specific computer programs or services might be mentioned in passing, but the lectures are not intended to give advice on current computer programs. 

This first mini course will cover linear-time exact pattern matching using the Z-algorithm. Use of k-mers. Dynamic Programming for alignment (both global and local) of two sequences, extension of the biological model to gaps.

The second session of this mini course will take place on Tuesday, January 19 from 11:00 am – 12:00 pm; the third session of this mini course will take place on Tuesday, January 19 from 1:30 pm – 2:30 pm; the fourth session of this mini course will take place on Tuesday, January 19 from 3:00 pm – 4:00 pm.