BIO/CSC295 2009F, Class 02: What is Bioinformatics? (2)

Admin:
* Please fill out the RISC Survey asap.
* For Thursday, do a peer review of two of your colleagues' response papers.  (Details to follow in class.)
* We will start the Web exploration in class today and continue it on Thursday.  You and your partner(s) should turn in answers to the Web exploration questions next Tuesday.

Overview:
* Dinosaur Peptides, revisited.
* What is bioinformatics?, revisited.
* The joys of interdisciplinarity.
* Web exploration.

Dinosaur Peptides:
* Summary: Fragments of peptides from T-Rex look like chicken
* Mass Spec Process:
  * Collect bone -> Dissolve -> Capillary tube (liquid chromatography)
    -> Collect fractions
  * Note: Bone is a complex mixture, the fractions are relatively simple
    mixtures
  * Ionize fractions and put them through a magnetic field.  The order
    they come out is based on mass/charge ratio.
* Bad Sam inturrupts: Didn't they do different things for the dinosaur bone?
  * Because of rusty stuff, they did chromatography
  * [Sam was thinking that they also did much more replication.]
* What does figure 1 say
  * 1A: Create a theoretical sequence
    * Start with collagen from a few other related species
    * Look for mistmatches
    * What do you do?
      * If there's a majority
    * Questions: 
      * Why these species?
        * They were available
      * How do we know that the result of this process results in a
        functional peptide?