CGS 5991: Bioinformatics Tools [2 credits]
Fall 2003
Instructor
Information
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Instructor: Giri Narasimhan, ECS 389, Phone x-3748, Office Hours: Thursday 11AM - 12:30 PM.
Course Web Page: http://www.cs.fiu.edu/~giri/teach/5991F03.html
Evaluation |
Exams: 20%
Homework: 20%
Semester Project: 50%
Class Participation: 10%
Justification
& Course Overview
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This is an introductory graduate course in the use of Bioinformatics tools. It is meant for graduate students whose major is not Computer Science. No background in Computer Science will be expected. The idea is to introduce students to standard tools and techniques used in Bioinformatics. Targeted students include graduate students doing research in many areas of Biological Sciences such as Moleclular Biology, Immunology, Cell Biology, Biochemistry, and Pharmacology.
Prerequisite
Knowledge
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Introductory graduate course in Molecular Biology (PCB 6025 or equivalent), or permission of instructor.
Topics |
·
Fundamentals of
Biology, Statistics, and the Internet
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Overview of
Bioinformatics, Computational Biology and Biotechnology
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Databases &
Software Packages: GenBank, SWISSPROT, BioPerl, BioJava.
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Sequence
Alignment & Multiple Sequence Alignment: BLAST, CLUSTAL.
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Phylogenetic
Analysis: CLUSTALW, Phylip, PAUP.
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Sequencing and
Mapping.
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Pattern
Discovery Techniques: TEIRESIAS, GYM.
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Machine
Learning & Predictive Methods: Neural Networks, Hidden Markov Models
(HMMPro), Self-Organizing Maps (GeneCluster), Support Vector Machines.
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Molecular
Structural Alignment, Analysis & Visualization: DALI, RASMOL, CN3D
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Microarray Data
Analysis: CLUSTER, SAM, GeneCluster, TreeView.
Evaluation will include several homework assignments, exams, and a semester project.
Texts and/or
References
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·
Bioinformatics:
A Practical Guide to the Analysis of Genes and Proteins, Eds. A. D. Baxevanis and B. F. Ouellette,
Wiley Interscience, 2nd ed., 2001. ISBN: 0471383910
·
Bioinformatics
– Sequence & Genome Analysis, David Mount, CSHL Press, 2002, Paperback, ISBN: 0879696087
Meeting
Times: The course will meet Tuesdays from 11:00 AM to 12:40 PM.