#
*640:338:01 Discrete and Probabilistic Models in
Biology*

Spring 02

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*IMPORTANT! This is the NEW Math 338.
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General Information

See the Main course page for general information
about this course.

**THE SPRING 2002 **semester
will focus on probabilistic and
dynamic programming methods in the analysis of
biological sequences. This is the first time that
the course is being offered and the syllabus is
an experiment. It may contain more than we can
actually do so we may end up editing it as we go along.
But I hope we can hit all the high points.

The first part of the course
is an introduction; we
study elementary
probability models arising in coverage analysis of
DNA sequencing strategies, and we introduce the basic
statistical notions of hypothesis testing and maximum
likelihood estimation. The probability models will give
an opportunity to review the use of important models and
techniques from probability and to introduce the Poisson process.
This part of the course will rely on class lecture notes
and handouts.

The second part of the course will study alignment of
biological sequences using Markov chains and dynamic programming.
Dynamic programming will be introduced as a technique for
solving the combinatorial optimization problem of optimal
alignment. Markov chains and hidden Markov chains are defined
at an elementary level and explored as models for sequences and
for study of alignment. This part of the course will be
based on chapters 2-6 of the text.

The final part of the course will feature more advanced
Markov chain theory; possible applications are to models for
evolution of sequences, the BLAST search method, and
some elementary population genetics models.

This course will be more lecture driven than text driven.
Much of the course will develop material outside of the text.
The text has much interesting material, but does not cover
all the topics of interests and lacks some of the mathematical
development needed.

- Class time and place: Tuesday/Thursday 4:30-5:50 PM (6th period), in
SEC-218
- Text:
Durbin, Eddy, Krogh, and Mitchinson, Biological Sequence Analysis:
Probabilistic models of proteins and nucleic acids, Cambridge University
Press, 1998; ISBN: 0 521 62971 3.
- Instructor:
Daniel Ocone -
518 Hill
Center - ocone@math. Office hours:
T5, Th2, or by appointment.
- Teaching Assistant. Pieter Blue. Office hours, M6, Th4 in Hill, 624.

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*Information and Resources*

Syllabus and homework assignments
Course notes and handouts

Problem solutions and lecture slides; an additional
link for Additional problem solutions,
Problem Sets 1-4.