Advanced Sequence Analysis in Bioinformatics
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Next Offering
Fall 2002. Eight meetings on Monday evenings, 6-9 pm, Cupertino, starting September 16.
Enrollment is open. Visit
UCSC extension web site .
Course Description
Large-scale sequencing efforts are producing enormous amounts
of data. Computational methods are essential for "mining" this data
to glean biological insights from it. This advanced course covers cutting-edge
methods that are more sophisticated and powerful than the simple methods
commonly
used for pairwise alignment, multiple alignment, and phylogenetic tree
construction. Topics covered include Hidden Markov Models for pairwise
alignment, for multiple alignment, for gene finding, and for conducting
profile-based searches; probabilistic methods for phylogenetic analysis;
stochastic context-free grammars for RNA analysis; and methods for conducting
ultra-fast database searches.
With an emphasis on in-depth computational methods and algorithms, this
course is geared towards the developer. Interested non-developers are welcome too!
Text
The required text is
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
,
R. Durbin et al, Cambridge University Press.
Prerequisites
Familiarity with vector and matrix notation, as acquired from a course in matrix
or linear algebra. Computational maturity, as acquired from a first course in
computer science.
Some familiarity with DNA and protein sequences.
Familiarity with probability and statistics basics, as acquired from the course
Data analysis, modeling, and visualization for bioinformatics.