BIOL-4534/CSCI-4931

INTRODUCTION TO BIOINFORMATICS

Room- B3324

Wednesdays 4:00-6:50 pm

Course Goals

This course introduces the students to Bioinformatics, which uses computer databases to store, retrieve and assist in understanding biological information. Genome-scale sequencing projects have led to an explosion of genetic sequences available for automated analysis. These gene sequences are the codes, which direct the production of proteins that in turn regulate all life processes. The students will be shown how these sequences can lead to a much fuller understanding of many biological processes allowing pharmaceutical and biotechnology companies to determine for example new drug targets. Students will be introduced to the basic concepts behind Bioinformatics and Computational Biology tools. Hands-on sessions will familiarize students with the details and use of the most commonly used online tools and resources. The course will cover the use of NCBI's Entrez, BLAST, PSI-BLAST, FASTA, ClustalW, Pfam, PRINTS, BLOCKS, Prosite and the PDB. An introduction to basic molecular biology, database design and the principles of programming languages will be provided.

Course Objectives:

At the end of the course the students should be able to:

1) Understand the basic terminologies in Bioinformatics

2) Learn some basic algorithms used in sequence similarity analysis.

3) Use biological databases available through Internet.

4) Write small programs in Bioinformatics using these databases.

Course Prerequisite:

Students should have basic skills for using the computer.

Course Methodology:

The course is designed for students from both biology and computer science background. Initial lectures will introduce students with basic concepts in computer science and biology. Learning algorithms and database concepts in Bioinformatics will follow this.

Appraisal:

Exams (Mid term and Final) 50%

Assignments 20%

Quizzes 10%

Group presentations 15%

Attendance 5%

Grading Scale

93+ = A; 90+ = A-; 87+ = B+; 83+ = B; 80+ = B-; 77+ = C+;
73+ = C; 70+ = C-; 67+ = D+; 63+ = D; 60+ = D-; 0+ = F

Required Textbook:

“Introduction to Bioinformatics: A Theoretical and Practical Approach”

By Stephen A. Karwetz and David D. Womble. Humanna Press.

Reference Book:

“Bioinformatics Computer Skill” by Gibas and Jambeck. O’Reilly press.

“Bioinformatics – Sequence and Genome Analysis” by David W. Mount, Cold spring Harbor Laboratory Press.

“Bioinformatics- A Practical Guide to the Analysis of Genes and Proteins” by

Baxevanis and Ouellette.

Office Hours.

Monday (3:00 PM to 4.00 PM) or based on appointment.

Contact information:

Email to M. Bazlur Rashid:

Or call 281-283-3756

Tentative Syllabus

Fundamentals of Bioinformatics and Information Technology

·  Introduction to Bioinformatics- What is it? Why needed? Potential?

·  Experimental sources of biological data

·  Publicly available databases and servers

·  Operating systems.

·  Internet tools

Biology Students / Computer Science Students
Intro to Programming and Databases
Goal: Introduce concepts of programming and DB technology.
·  Fundamental principles of programming
·  Object-oriented programming using Java Introduction to databases
·  SQL / Intro to Molecular Biology
Goal: Explain the basic concept of molecular biology to computer science students.
·  Cell, Molecule, Gene, Chromosome, DNA, RNA
·  Protein, Connection DNA-RNA-Protein, Protein structures and functions
·  Bio-chemical properties of amino acids, Motif, Domain
·  Protein Families, Evolution, Similarity and Homology.

Assignment I

Bioinformatics Tools for Genome Analysis(Both groups converge)

Goal: To introduce the most important Bioinformatics software tools, and explains the principles and algorithms that underpins them

·  High throughput sequencing and sequence analysis

·  Pair wise alignment and database searching

·  Gene Finders and Feature analysis

·  Algorithms for finding Transcriptional Regulatory Signals

·  Comparative Genomics and phylogenetic analysis

Assignment II

Midterm Exam!!

Computational analysis of protein structure and functions

Goal: To understand the computational approach of protein classification and structure predication

·  Multiple alignments of protein sequences

·  Methods for pair wise alignment and motif discovery

·  Searching for homology in protein sequence databases.

·  Algorithms for predication of secondary and 3D structure or proteins.

·  Application of Neural Networks in protein structure prediction

Assignment III

Applications and Commercial Aspects of Bioinformatics

Goal: To outline the current and potential applications of bioinformatics and the legal, ethical and commercial aspects of using biological data.

·  Drug discovery

·  Genetic basis of disease

·  Personalized medicine and gene-based diagnostics

·  Legal, ethical and commercial ramifications of bioinformatics

PERL Programming to Facilitate Biological Analysis

Goal: To provide students with the ability to program in PERL, the most popular programming language in the bioinformatics community.

PERL programming for:

·  Data manipulation

·  File maintenance

·  Regular Expression

·  Application of Perl in Bioinformatics

Assignment IV

Computational Tools for Expression Analysis

Goal: To provide an understanding of Microarray technology and its implications in the health care industry.

·  Microarray Technology

·  DNA and Protein microarrays

·  Analysis of expression array data using available software

·  Gene expression informatics

Bioinformatics Research

Goal: To equip students with the skills and understanding required beginning a career in bioinformatics research.

·  How to carry out research - with a particular emphasis on computer-based research

·  Introduction of the general research topics in Bioinformatics

·  Recent discoveries using Bioinformatics.

Intro to Bioinformatics

Tentative Schedule

Spring 2007

Date

/ /

Topic

January 17 / Lecture 1 / Introduction
January 24 / Lecture 2 / Chapter 2
January 31 / Lecture 3 / Chapter 4
February 07 / Lecture 4 / Chapter 5
February 14 / Lecture 5 / NCBI databases and programs
Assignment #1 due
February 21 / Lecture 6 / Sequence alignment algorithm
Chapter 27 and handouts
February 28 / Lecture 7 / BLAST algorithm
March 07 / Mid-term / Assignment #2 due
March 14 / Spring Break
March 21 / Lecture 8 / FASTA algorithm
March 28 / Lecture 9 / Phylogenetic analysis
Assignment #3 due
April 04 / Lecture 10 / Phylogenetic analysis
April 11 / Lecture 11 / Chapter 34
DNA micro-array analysis
April 18 / Lecture 12 / Predicting structure of proteins
April 25 / Review
Assignment #4 due
May 02 / FINAL