CSCI 4964 Bioinformatics: Algorithms and Systems

Spring 2003

Contact Information
Instructor:  Mohammed J. Zaki
Office:  Lally 307
Phone:   x6340
Email:  zaki.AT.cs.rpi.edu
Class Hours: Low 4034, MR 10-11:50am
Office Hours: Mondays 12-2pm, or by appointment
Web Page:  http://www.cs.rpi.edu/~zaki/bioinfo/
Course Information

  • Course Syllabus
  • Useful Bioinformatics Links

    Announcements

  • April 27th: CURRENT GRADES have been posted.

  • April 22nd: HW3 solution is available.

  • April 22nd: GeneExpression Slides are available. This talk was given by Dr. T.M. Murali (Boston U) at RPI CS Colloquium.

  • April 11th: HW3 is available. Due date is Mon, 21st April, in class. Submit a hard copy. No late assignments allowed.

  • March 26th: HW1 Solution has been posted. getseq.pl is the program that extracts the protein sequence (using bioperl functionality), and align.pl performs the alignment.

  • MArch 4th: HW2 Solution has been posted.

  • Feb 28th: PAPER . Please read this paper before 17th March, when Chip Lawrence will be taking about it.

  • Feb 22nd: Tutorial on HMMs by Rabiner is available by clicking on the link. Another intro is the paper by Rabiner and Juang in IEEE ASSP Magazine, Jan 1986, pages 4-16, titled "An introduction to HMMS". This may be available in our library.

  • Feb 19th: Assignment 2 is now available. NEW Due date is 3rd March (monday).

  • Jan 30th: Assigment 1 is now available. Due date is 13th Feb (extended). You may find the tutorial at the following link of use in extracting the protein seq and translation: http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/. More documentation is available at the bioperl.org site.

    Class Topics

    MONDAYS THURSDAYS
    Jan 13 - Overview Jan 16 - Sequence Databases
    Jan 20 - Martin Luther King, Jr. Day (No Class) Jan 23 - Pairwise Alignment
    Jan 27 - Pairwise Alignment Jan 30 - Substitution Matrices
    Feb 3 - Substitution Matrices Feb 6 - Multiple Sequence Alignment
    Feb 10 - Multiple Sequence Alignment Feb 13 - Multiple Sequence Alignment
    Feb 18(Tue) - Hidden Markov Models Feb 20 - Hidden Markov Models
    Feb 24 - Hidden Markov Models Feb 27 - Sequence Similarity
    Mar 3 - Microarray Analysis (Guest Lecture) Mar 6 - EXAM I
    Mar 10 - Spring Break Mar 13 - Spring Break
    Mar 17 - No class Mar 20 - Proteins (Guest LEcture)
    Mar 24 - Phylogenetic Trees Mar 27 - Phylogenetic Trees
    Mar 31 - Database Searches Apr 3 - Database Searches
    Apr 7 - Protein Structure Apr 10 - Protein Structure
    Apr 14 - Protein Strucutre Apr 17 - Gene Finding
    Apr 21 - Gene Finding Apr 24 - EXAM II
    Apr 28 - Whole Genome Analysis May 1 - No Class
    Number of Visitors