CAP 5510 & CGS 5166: Spring 2007
Bioinformatics Course Homepage
Tue & Thu 11:00 - 12:15, ECS 141

• Apr 26: End-of-Semester "pot-luck" party starting 7:30 PM. Location: 4201 Collins Avenue #1801 Miami Beach. Party starts late to accomodate students who have an exam until 9PM. It's fine to come late.
• Apr 11: Presentation schedule
  Thursday 4/12: Adam/Olga, Ricardo;
  Tuesday 4/17 (start at 10:30 AM): , SamidhSajib, Shilpa/Valli, Stacey;
  Thursday 4/19: Xiaoli, Pat, Andres
  Attendance at the presentations is mandatory for the entire class. You will need to contact me in advance at x3748 if you have a good reason not to be able to attend.
  A preliminary report of the work was due on April 10. A final report of your work is now due on Monday, Apr 23 by 5:00 PM.
• Apr 03: No class today. We will meet on Apr 05, Thursday.
• Mar 02: Homework 2 is due on March 13i instead of Mar 6.
• Feb 20: Homework 2 is now ready. See below.
• Jan 20: Collaboration Policy for homework assignments: The work has to be your own. You may discuss with classmates or friends and get minor pointers. But the bulk of the work has to be your own. Copying portions of someone else's work is not allowed. The written part of the assignment has to be in your own words. Any evidence of violation of this policy will be dealt with severely. I implicitly trust you. Do not abuse this trust! If you have questions and/or doubts, ask me in class or email me.
• Jan 20: Homework 1 is now ready. See below.
• Jan 17: Read Chapter 18 from Baxevanis and Ouelette before class and familiarize yourself with Perl.
• Jan 17: Note the change in my office room number.
• Jan 16: Tuesday lectures will start at 10:30 AM starting today (Jan 16). Make sure you are on time!
• Jan 3: Note that the class will meet in room ECS 141, and not in the PC building, as suggested by Panthersoft.
• Jan 3: If you are interested in research in this area, please visit the website for the Bioinformatics Research Group @ FIU.

• For CS Majors: CAP 5510
• For NON-CS Students: CGS 5166

• Bioinformatics, by David Mount, CSHL Press, 2002, 2nd Edition, Paperback, ISBN: 0-879-69712-1
• Bioinformatics, by Baxevanis & Ouelette, 3rd Edition, ISBN: 0-471-47878-4.

• Homework 1 (Due Feb 6, 2007);
• Homework 2 (Due Mar 6, 2007);

• Jan 9: Lec 1[pdf] [Introduction & Motivation]; Reading: [Chapters 1, 2 (from DM); Extra]
• Jan 11: Lec 2[pdf] [Motivation & Biological Preliminaries]; Reading: [Same as Above]
• Jan 16: Lec 3[pdf] [Biological Preliminaries]; Reading: [Same as Above]
• Jan 18: Lec 4[pdf] [Perl & BioPerl]; Reading: [Chapter 18 (from BO); Chapter 12 (from DM)]
• Jan 23: Lec 5[pdf] [Sequence Alignment & BLAST]; Reading: [Chapter 11 (from BO); Chapter 3 (from DM); Extra]
• Jan 25: Lec 6[pdf] [BLAST & Multiple Sequence Alignment]; Reading: [Chapter 12.1-12.4 (from BO); Chapter 6 (from DM)]
• Jan 30: Lec 7[pdf] [Multiple Sequence Alignment & Suffix Trees]; Reading: [See Chapter 4 (from DM) for Statistics of alignments; Chapter 5 (from DM) until page 189]
• Feb 1: Lec 8[pdf] [Profiles & Hidden Markov Models]; Reading: [Chapter 5 (from DM) from page 189 to end; Box 8.2 (from BO)]
• Feb 6: Lec 9[pdf] [Hidden Markov Models & Applications; Motif Detection]; Reading: []
• Feb 8: Lec 10[pdf] [Pattern Discovery and Motif Detection]; Reading: []
• Feb 13: Lec 11[pdf] [DNA Motif Detection]; Reading: []
• Feb 15: Lec 12pdf] [EM Algorithm, Protein Structure]; Reading: []
• Feb 20: Lec 13pdf] [Protein Structure Prediction]; Reading: []
• Feb 22, 27, Mar 1, 6: Lec 14pdf] [Gene Expression, Microarray Data Analysis]; Reading: []
• Mar 8,13: Lec 15pdf] []

• Popular [Posted Jan 9]: California Sea urchin genome sequenced, Nov 2006.