ECS 224 Fall 2009 - String Algorithms and Algrorithms in Computational Biology (original) (raw)
This index page will just link to the various course handouts that are available on the web, and provide some description of them.
Distribution List
Class tuesday Oct. 11 is cancelled. Watch the video on least common ancestor algorithm. Class on thursday is scheduled as normal - unless you hear from me.
The linear-time construction algorithm for suffix arrays we discussed in class is discussed in a more general setting in "Linear work suffix array construction", Journal of the ACM (JACM), Volume 53 , Issue 6, November 2006, Pages: 918 - 936.
list of links to videos of lectures for CS 222A Fall 2007 The Lecture on November 21 is on the Z-algorithm. The Lecture on November 30 and the start of the Lecture on December 3 cover a linear-time preprocessing, constant-time lookup algorithm for the Least Common Ancestor (LCA) in a tree.
We will not discuss edit distance and string alignment in detail in this class, since most people have already been exposed to these topics, and because they have simple solutions via DP (the local alignment problem is more complex). If you have never seen the DP for alignment or edit distance, see the video lecture of Oct. 8 2007 in the cs 222A videos. Or, see the videos posted for CS 124, lectures 5 through 11.
Notes on the Perfect Phylogeny Problem This is an extended version of the notes put here earlier. Sections on The Splits Equivalence Theorem and 3-state perfect phylogeny were added to the original notes October 22.
As mentioned in class, good sources of papers in combinatorial string and computational biology algorithms are: the Combinatorial Pattern Matching (CPM) Conference, the Workshop on Algorithms in Bioinformatics (WABI) Conference, the ISBRA (International Symposium on Bioinformatics Research and Applications) Conference.
