CS 461b/661b: Bioinformatics Tools and Applications

 

Description

This course provides an introduction to several common types bioinformatics software tools used in biology research.  The necessary biology background, the computational methods (algorithms), and the user interface will be introduced for each software tool studied in the course.  Students will have hand-on experience of several software tools and gain some experience on developing bioinformatics software through a course project.

Prerequisites:  Computer Science 331a/b and 340a/b; Biochemistry 280a is recommended.

Time and Venue: Monday 2:30-4:30 (MC320) and Wednesday 2:30-3:30 (MC320)

Course Outline

Office Hours:  Tuesday 4-5pm, Wednesday 4-5pm (MC362)

Lecturer: Bin Ma

News:

¡¤         The class on March 10 is moved to MC316 again because a failure of the projector in MC320.

¡¤         Final exam: April 25, 9am-11am with a possible one hour extension.

Assignment:

1.       Assignment one.  Due date: Feb. 11th. Course time.  Submit to the lecturer in the classroom.

2.       Assignment two.  Due date: March. 17th.  Course time.  Submit to the lecturer in the classroom.

Projects:

1.       You can choose a project from the course outline.

2.       Or you can choose a project this new list.

Course Notes:

1.       Introduction

2.       Whole-Genome-Shotgun Sequencing  (DIY: Assemble a small genome.)

3.       PCR and Primer Design and
an application, STR typing.

4.       Gene finding.  (DIY: Find a gene yourself.)

5.       Mass Spectrometry I: Basic data processing.

6.       Mass Fingerprint  (DIY: Understand MS data complexity and Mass fingerprint.) Feb. 13,2008)

7.       Tandem Mass Spectrometry (DIY: manual and auto analysis of ms/ms spectra, Feb. 20, 2008)

8.       Mass Spectrometry II (this obsoletes notes 7). (DIY: de novo sequencing error, SPIDER, and PTM)

9.       March 10: BLAST and PatternHunter.   (DIY: practice using Genbank and Blast)

10.   March 17: Protein Quantitation with Mass Spec, Mass Spec file formats.  (DIY: write a small program to compute seed sensitivity.)

11.   March 24: Fun stuff: Chain Letter, Kolmogrov Complexity, Whole Genome Phylogeny, Plagiarism Detection.  No course notes needed.

12.   March 31: this week¡¯s classes are moved.

13.   April 7, 9: student presentations

14.   April 14, 16: graduate students¡¯ presentations