[Colloquium] Reminder: Guest Speaker @ TTI-C Today (3/14/06)

[Katherine Cumming]

**********TTI-C Guest Speaker Today***********
                          March 14, 2006
        Presented by:  Toyota Technological Institute at Chicago
 
Speaker:  Brona Brejova, University of Waterloo
Speaker's home page:  <http://www.bioinformatics.uwaterloo.ca/~bbrejova/>
http://www.bioinformatics.uwaterloo.ca/~bbrejova/
 
Date: Tuesday, March 14, 2006 
Location: TTI-C Conference Room
Time:  10:00 am
 
Title:   Knowing More about Alignments Helps in Finding Them
Abstract:
The local alignment problem is the task of finding pairs of similar
substrings in a large DNA or protein sequence database.  It is one of the
basic steps in analyzing a new sequence.  Alignments of similar sequences
highlight areas preserved by evolution and help to determine structure and
biological function of sequences.  Increasing amount of available genomic
sequence data creates the need for further improvements in efficiency and
accuracy of local alignment tools.

We explore the technique of spaced seeds (developed by Ma, Tromp, and Li in
2002) for increasing the accuracy of a commonly used heuristic local
alignment algorithm by tuning a certain parameter called spaced seed.  We
argue that the spaced seed should be optimized with respect to a realistic
probabilistic model of biologically meaningful alignments.  The seeds that
we discover significantly improve the accuracy and running time of local
alignment for protein coding regions in DNA.  We also generalize the notion
of spaced seed to encompass several approaches suggested by other
researchers.  This unifying framework allows the extension of our ideas to
protein sequences.

This is joint work with Dan Brown and Tomas Vinar. 
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If you have questions, or would like to meet the speaker, please contact
Katherine at 773-834-1994 or kcumming at tti-c.org.   
For information on future TTI-C talks and events, please go to the TTI-C
Events page:  http://www.tti-c.org/events.html.  TTI-C (1427 East 60th
Street, Chicago, IL  60637)
 
 
 
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