Visualizing BLAST (FWIW)

Presentation Overview

• What is BLAST?
• Why Visualize?
• Previous Work
• Current and Future Work
• A Plea for Feedback

What is BLAST?

• Find sequence alignments (nucleotide, protein)
  • Basic · Local · Alignment · Search · Tool
• Published in 1990 by NCBI
  • Faster than FASTA
  • Better statistics than FASTA
• Not dead yet!
  • Default tool
  • Many databases
  • WU-BLAST 2
  • PSI-BLAST

Why Visualize?

• Text can be overwhelming
  • Example
  • Many types of data intermingled
    • Direction, Length, Score, Clusters, Gaps
  • Limited conveyance via ASCII
• Leverage human visual perception
  • Example
  • Pre-attentive processing
  • "Pop out" useful information
  • Length, orientation, contrast, curvature, shape, hue

Previous Work

• NCBI
  • 
• TAIR, SGD
  • 
  • Cleaner, Name, P-value, Direction, Hit+HSPs, Bucketing, Date

Current and Future Work

• Improvements
  • Expanding buckets
  • Conduct more user studies
  • Degrade gracefully
• Befriend the color blind
  • Example problem
• Metrics for visual displays
  • Review against best practices
• Bling-bling
  • Animation
  • Stereoscopy
  • 3D (just kidding)

A Plea for Feedback

• Do you use BLAST?
• Have any friends using BLAST?
• Complaints?
• Ideas!

The End

• Thanks for your support