CIS 529: Bioinformatics

Welcome to the course of Bioinformatics!
Bioinformatics [http://faculty.pieas.edu.pk/fayyaz/bioinfo.html] is the field of study aimed at solving problems in biology using computing. Research and development in biology is occurring at an ever increasing pace. Due to the nature of biological data, computing algorithms are critical to
help understand it. Here [http://faculty.pieas.edu.pk/fayyaz/bioinfo.html#reasonsforacomputerscientisttobeengagedinbioinformaticsresearch] are some reasons why computer scientists should learn Bioinformatics!

This course is designed as an introductory graduate or senior undergraduate course for computer science students who plan on working in Bioinformatics. At the conclusion of this course,
successful students will:

Know how computing can be and is being applied to problems in biology

Be able to use existing tools for analysing biological data

Understand the working of different bioinformatics algorithms

be in a position to take more advanced courses in Bioinformatics for algorithmic development

Broadly speaking, this course is divided in two major parts: Sequence analysis and structure analysis. We shall cover sequencing technologies, alignment algorithms, phylogenetics as well as structural proteomics!

Prerequisites
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Good programming skills in any high level language

Understanding of computing data structures, algorithms and algorithm analysis

No Biology knowledge is required


Topics
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Bioinformatics: Breadth and depth
Basics of Molecular Biology
Sequence Alignment: NW
Sequence Alignment: SW
Sequence Alignment: Affine Gap Penalties, Substitution Matrices
Tools for Sequence Alignment
Multiple Sequence Alignments
Detecting remote homology
Phylogenetics
Introduction to Sequencing
Assembly Algorithms
Read Mapping
Introduction to Proteomics
Computational problems in proteomics
Protein structure determination & databases
PyMOL
Protein structure prediction
Protein Interface Prediction

Textbooks
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Jones, Neil C., and Pavel A. Pevzner. An Introduction to Bioinformatics Algorithms.Cambridge, MA: The MIT Pres.

Gu, Jenny, and Philip E. Bourne. Structural Bioinformatics. John Wiley & Sons, 2011.

Kessel, Amit, and Nir BenTal. Introduction to Proteins: Structure, Function, and Motion. Taylor & Francis US, 2010.

Course notes will be provided

Grading policy:
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(Tentative)
Quizzes/Reading: 5%
Assignments: 25% (tentatively 5 Assignments)
Programming/software based
Sessional-I: 10%
Sessional-II: 10%
Bonus Marks: Class Questions
Final Exam: 50%