Downloads

Update: November 10th, 2009

Homeworks

Projects

  1. Pengcheng
    October 15th, 2009 at 22:25
    Quote | #1

    fot the input data (zip format), the directory proj1_data have no file in it(size 0!)

  2. nils
    October 16th, 2009 at 09:32
    Quote | #2

    The zip data has been updated for Windows users.

  3. C260A Intro Bioinformatics » Homework 4 Solutions
    November 4th, 2009 at 14:44
    #3
  4. Pengcheng
    November 10th, 2009 at 17:54
    Quote | #4

    For project 2,
    what does * column define in the input sm files?

  5. nils
    November 10th, 2009 at 19:28
    Quote | #5

    The * column means anything else (not one of the 20 amino acids). This can occur if the amino acid could not be determined.

  6. Shaun Taylor
    November 13th, 2009 at 23:36
    Quote | #6

    The instructions say to submit as project 1. Minor detail but will screw up an email filter you may have set up.

  7. Shaun Taylor
    November 14th, 2009 at 01:09
    Quote | #7

    In your sample output file, the first character on your local match is a mismatch. I implemented the algorithm as described in class and my algorithm gets identical scores as yours, but omits that first mismatched character (basically starts with “LTPEEK”). Is this a bug in the algorithm that generated the sample code? It seems the behavior in my program is more correct than the sample output in this case.

  8. nils
    November 14th, 2009 at 12:12
    Quote | #8

    Shaun Taylor:
    The instructions say to submit as project 1. Minor detail but will screw up an email filter you may have set up.

    Fixed, thanks!

    Shaun Taylor:
    In your sample output file, the first character on your local match is a mismatch. I implemented the algorithm as described in class and my algorithm gets identical scores as yours, but omits that first mismatched character (basically starts with “LTPEEK”). Is this a bug in the algorithm that generated the sample code? It seems the behavior in my program is more correct than the sample output in this case.

    See the discussion on the Project 2 post. This is the downloads page.