Scribe: D. Slotta

Today's Handouts and Announcements

• None

Today's Topics

• Fragment Assembly (cont')
  • Heuristics (SM p.132)
    • Objective Function:
      1. Column consistency (entropy)
      2. Coverage of columns
      3. Linkage - Good Overlaps

    • Calculate score for n² overlaps (dynamic programming) (SM p.135)

• Physical Mapping of DNA - Where are the Genes?
  • Biological ways of getting at a map:
    • DNA Marker - short, precise DNA sequence
    • Oligonucleotides - manufactured short sequences of DNA (20bp max)
    • Restriction Enzymes - cut DNA at precise subsequences

  • Double Digest Problem (SM p.145)

  • Hybridization Mapping (SM p.146)

Today's Sources

• Setubal and Meidanis: Chapters 4 & 5.