UA Biocomputing seminar
    
       Identifying and Visualizing Patterns in Genomic DNA Sequence

Airlia Thompson / MCB

Friday, Sept 23, 3:00-4:30. 
Gould Simpson Building, 701 

Comparing genomic data between species can lead to insights into evolutionary
events.  Gene duplication and chromosomal rearrangements occur over time and
create a roadmap of sorts. Dr. Gio Bosco and Airlia Thompson of the MCB
department are interested in looking for specific short DNA motifs as single
occurrences or in tandem repeats in Drosophila genomic data.  While we have
found software that locates the patterns of interest, it has been quite a
challenge to try to visualize the motifs (ranging from 5 to 10 bases in length)
on a chromosomal scale (approximately 30Mb).  A typical output from the
motif-finding programs consists of about 3 million data points.  We have used
Ggobi, OpenDX, and Amira for visualization but as yet have not found a helpful
way to see pattern similarities.  We would like to discuss other possibilities
for identifying patterns in large data sets.