ECS 124 - Foundations of Algorithms for Bioinformatics - Dan Gusfield
This page links to the videos of course lectures. These videos were mostly made in 2002 and edited and somewhat extended in 2014.
Despite their age, and despite the fact that *software, databases, websites, and data* in bioinformatics change rapidly,
the topics included are still of current importance. This is because the emphasis in the lectures is on
fundamental algorithms and analyses which already stood the test of time in 2002, and have continued to do so. Of course,
there are some new topics in bioinformatics algorithms that were not of perceived importance in 2002, and hence are not
covered by these lectures, but they are surprisingly few.
An overview of each of the lectures
Topics by date
Introduction to the course and to bioinformatics.
Further introduction to bioinformatics, and the value of computing.
How to define sequence similarity.
Extensions to the model of sequence similarity
Computing sequence similarity.
Computing sequence similarity using an alignment graph.
From alignment graphs to formal Dynamic Programming.
Sequence alignment using Dynamic Programming - continued.
Local sequence alignment.
End-gap-free alignment and whole-genome shotgun sequencing.
Expected lengths of the longest common subsequence and substring.
Expected length of the longest common subsequence.
Expected length of the longest common substring.
Expected length of the longest common substring II.