CS5238: Advanced Combinatorial methods in bioinformatics

201l/2012 Semester 1

Time: Monday (6:30 to 8:30pm), LT15

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: Monday (5:00 to 6:30pm)
Office: COM2 #02-06

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
18 Aug 2011 No class
215 Aug 2011 Basics of Molecular Biology
322 Aug 2011 Sequence comparison
429 Aug 2011 Suffix tree (1)
55 Sept 2011 Suffix tree (2)
612 Sept 2011 Genome Assembly (1)
19 Sept 2011 Genome Assembly (2) Recess week
726 Sept 2011 Midterm
83 Oct 2011 Motif finding (1)
910 Oct 2011 Motif finding (2)
1017 Oct 2011 Motif finding (3)
1124 Oct 2011 RNA secondary structure prediction
1231 Oct 2011 RNA secondary structure comparison
137 Nov 2011 Project Presentation
12 Nov 2011 Reading period
1 Dec 2011 Examination

For powerpoint slide, please get it from IVLE website.


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