CS 224 Fall 2011 String Algorithms and  Algorithms in Computational
Biology - Tues, Thurs 1:40 - 3:00 244 Olson

Dan Gusfield


There is also a discussion section that may (possibly) be used for
student presentations at the end of the quarter.  We will schedule that
later if needed.  Otherwise there will be no discussion section. 


The formal prerequisite of this class is CS 222A. But, whether you have
had that course or not, what is critical is that you understand the
basic game-plan of worst-case algorithm analysis, that you can think
about algorithms without the need to see low-level programming details,
and that you can follow and construct proofs of algorithmic properties.
The focus of the class is on algorithms that illustrate techniques and
problems that are relevant in computational biology, but it is not a
course on practical computational biology or bioinformatics. That
course is CS 124, which is not a prerequisite for CS 224.

The class will be a mixture of three major topic areas: 1) string
algorithms, particularly based on suffix arrays and trees 
2) algorithms and
combinatorial structure for phylogenetic networks (for this topic we
will refer to the recent book ``Phylogenetic Networks" by Huson et al.
3)
algorithms to deduce phylogenetic networks involving recombination as
well as mutation. 

In all three areas of concentration, algorithmic
efficiency and combinatorial structure will be emphasized. The
phylogenetic topics also discuss combinatorial optimization methods and
integer programming.

Open problems will be identified. In the five times that this class has
been offered, at least two published papers resulted from open problems
examined in the class.

There will be regular homeworks and a final exam (most likely
take-home). 


Depending on enrollment etc. students may also have the opportunity to read a current paper
(I will suggest some later), and present it in the scheduled discussion
section. The following lecture topic list is subject to revision as we
go. There is no assigned textbook but the Huson book mentioned above will be used for
the second part of the course (get it through Amazon). Course notes or copied materials
will be handed out on the other topics.

The main topics are:

1.  Non-trivial applications of dynamic programming: hybrid dynamic
programming with suffix trees, linear space applications, four Russians
algorithms, improvements in RNA folding algorithms, circular string
edit distance.

2. Linear-time construction of suffix
trees, suffix arrays, and LCP information; 
linear-time preprocessing methods for constant-time least common
ancestor and least common extension queries.  Many possible
applications such as rapid identification of pathogens,  finding all
tandem repeats in linear time, use of LCA for accumulating common
substring statistics, approximate tandem repeat finding, fast unique
decipherability using suffix trees, LZ sequence compression.

3. The Burrows-Wheeler transform and its use in sequence analysis in computational
biology.

4. Phylogenetic Networks as treated in Huson's book.

5. Phylogenetic Networks involving recombination: galled-trees,
decomposition, construction of good networks, lower bounds on the
number of recombinations needed, many uses of integer programming,
applications to topics such as genome-wide association studies.
Phylogenetic networks involving hybridization and other reticulation
events; relation to SPR and maximum agreement forests.  Introduction to
the open field of extending the binary case to the multi-state case.