COURSE DESCRIPTION
Department and Course
Number
Course
Title
CS 440
Bioinformatics I
Course
Coordinator
Total Credits
Contact Hours
Hill
3
37.5 hours (Lecture)
Current Catalog Description
Fundamental concepts of bioinformatics and use of bioinformatics tools from the
viewpoint of a bioinformaticist/biologist. Introduction to bioinformatics algorithms. This
course is the first of a two-course sequence CS440/CS441 that is designed to provide an
introduction to selected topics in bioinformatics. This course will emphasize the use of
bioinformatics tools as well as the underlying algorithms, but it is not a programming
course. Writing is an integral part of this course.
Textbooks
DNA: The Secret of Life by James D. Watson, Alfred A. Knopf, 2003.
References
Genes VII or GenesVIII by Benjamin Lewin. Oxford University Press. ISBN 0-19879276-X
Bioinformatics Sequence and Genome Analysis 2nd Edition by David W. Mount. Cold
Spring Harbor Laboratory Press, 2004. ISBN: 0-87969-712-1.
Medical Genetics by Jorde, Carey Bamshad and White. Mosby Publishing.
Computational Methods in Molecular Biology by Salzber, Searls, and Kasif. Elsevier.
The Phylogenetic Handbook. Edited by Marco Salemi and Anne-Mieke Vandamme.
Course Outcomes
This course is designed to introduce the student to the fundamental concepts of
bioinformatics and how it can be used as a tool by biologists as well as an area of
research in computer science.
Relationship between Course Outcomes and Program Outcomes: C, I, K
Prerequisites by Topic
Fundamental knowledge of computer science and biology.
Required/Elective: Elective
Major Topics Covered in the Course
1. Review of Biology
2. Sequence similarity
3. Scoring and substitutions matrices
4. Sequence Alignment
5. Global & Local Alignment by Dynamic programming
6.
7.
8.
9.
Multiple Sequence Alignment
Phylogenetics
Genomic Annotation
BLAST
Laboratory projects
Students are required to perform a number of exercises using web-based bioinformatics
tools and to write a short summary of each.
Criterion 3 Student Outcomes
Outcome
a
An ability to apply knowledge of computing and mathematics appropriate to the discipline
b
An ability to analyze a problem, and identify and define the computing requirements appropriate
to its solution
c
An ability to design, implement, and evaluate a computer-based system, process, component, or
program to meet desired needs
d
An ability to function effectively on teams to accomplish a common goal
e
An understanding of professional, ethical, legal, security and social issues and responsibilities
f
An ability to communicate effectively with a range of audiences
g
An ability to analyze the local and global impact of computing on individuals, organizations, and
society
h
Recognition of the need for and an ability to engage in continuing professional development
i
An ability to use current techniques, skills, and tools necessary for computing practice
j
An ability to apply mathematical foundations, algorithmic principles, and computer science
theory in the modeling and design of computer-based systems in a way that demonstrates
comprehension of the tradeoffs involved in design choices.
k
An ability to apply design and development principles in the construction of software systems of
varying complexity.
Oral and Written Communications
None
Social and Ethical Issues
None
X
X
X