CS5238: Advanced Combinatorial methods in bioinformatics

2009/2010 Semester 1

Time: Friday (6:30 to 8:30pm), LT19

Click here to visit the IVLE course webpage (that is the main page).


Instructor

Lecturer: Sung Wing Kin, Ken
Email: ksung@comp.nus.edu.sg
Consultation hours: Friday (5:00 to 6:30pm)
Office: COM1 #02-20

Aim and Objective

Biology data are too enormous. Handling them using brute-force approaches becomes impossible and efficient algorithms are required. This module has an in-depth study of some of these advance algorithms. Through the course, students not only are able to understand these algorithms in detail, but are also given chances to solve some research problems in this field.

Prerequisites: Pass CS3230 (Design and Analysis of Algorithms) or its equivalence. Note that students are expected to have good understanding in the analysis of algorithm (e.g. Recursion, Dynamic Programming, time complexity analysis, etc). From the past experience, students without good knowledge in algorithm cannot catch up with the pace of the module.

Supplementary Readings

Assessment

Syllabus (Tentative)

Week No. Date Topics Remark
114 Aug 2009 Basics of Molecular Biology
221 Aug 2009 Sequence comparison
328 Aug 2009 Multiple Sequence Alignment
44 Sept 2009 Suffix tree (1)
511 Sept 2009 Suffix tree (2)
618 Sept 2009 Database searching
25 Sept 2009 Recess week
72 Oct 2009 Midterm
89 Oct 2009 Motif finding (1)
916 Oct 2009 Motif finding (2)
1023 Oct 2009 Motif finding (3)
1130 Oct 2009 RNA secondary structure prediction
126 Nov 2009 RNA secondary structure comparison
1313 Nov 2009 Project Presentation
Nov 2009 Reading period
Nov 2009 Examination

Notes For powerpoint slide, please get it from IVLE website.

Old Notes

Project Group list


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