Computational Methods in Fragment Assembly
X459.7 Computer Science (.5)

The advances in DNA sequencing technologies over the past two decades
have revolutionized molecular biology.  One highly productive approach
is to sequence small DNA fragments, and use computer algorithms to
assemble them into much longer sequences.  This approach, called
shotgun sequencing, was used int he sequencing of the human genome by
the private sector.  The assembly approach also played a key role in
the construction of the publicly funded human genome sequence draft.
Computer assembly methods are also applicable to other sequencing
technologies such as sequencing by hybridization.  More generally,
these computational methods may be used in any situation in which one
has sequence fragments from an unknown sequence and wishes to
reconstruct the sequence from the fragments.  This short course covers
the fundamental algorithms used in sequence assembly.  The coverage
will be quantitative.  The actual algorithm used in the assembly of
the public human-genome draft will also be described.

Prerequisite: Some familiarity with algorithms, as acquired from a
first college-level course in data structures and algorithms.

ARUN JAGOTA, Ph.D., conducts research in neural networks and
bioinformatics at UCSC.  He has extensive experience in teaching a
variety of computer-science courses at various institutions, including
UCSC, UC Berkeley Extension and Santa Clara University.  He has worked
in both academia and industry, and is the editor-in-chief of the
journal <I> Neural Computing Surveys. </I>

Fee: $185 ($204 if registering after January 23, 2002).

CUPERTINO
3 meetings: Thursdays, 6-9 pm, February 6020.
UCSC Extension, 10420 Bubb Rd.

EDB 023X59 (use this EDP code to enroll)