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)
Assignments
Quizzes
Group presentations
Attendance
50%
20%
10%
15%
5%
Grading Scale
93+ = A;
73+ = C;
90+ = A-;
70+ = C-;
87+ = B+;
67+ = D+;
83+ = B;
63+ = D;
80+ = B-;
60+ = D-;
77+ = C+;
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: rashid@cl.uh.edu
Or call 281-283-3756
Tentative Syllabus
Fundamentals of Bioinformatics and Information Technology
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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
Intro to Programming and Databases
Goal: Introduce concepts of programming and DB
Computer Science Students
Intro to Molecular Biology
Goal: Explain the basic concept of molecular biology
technology.
 Fundamental principles of programming
 Object-oriented programming using Java
Introduction to databases
 SQL
to computer science students.
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Cell, Molecule, Gene, Chromosome, DNA,
RNA
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Protein, Connection DNA-RNA-Protein,
Protein structures and functions
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Bio-chemical properties of amino acids, Motif,
Domain
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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
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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
May 02
Review
Assignment #4 due
FINAL