CAP 5510 -Introduction to Bioinformatics

Fall 2009
MW 1:30 pm to 2:45 ENGR 20105 Main Campus(Orlando)
Key Code 88614

Prof. Amar Mukherjee
Office 304 HEC
Office and/or email hours: MW 2:45 to 4:00pm
Email Address: amar@cs.ucf.edu
Telephone: 407-823-2763

Academic Calendar

Methods of Evaluation (Subject to Change)
Homework Assignments 25%; Midterm(s): 20%; Term project: 20%; Final:35%
Grading: >95% is A; 90-95% A-; >85% B+, 82-85% B,80-81% B-
C and D grades are broken down similarly like B in the 70's and 60's percentages. Any score below 60% is F.

Final Exam Schedule

Background:

Bioinformatics and Computational Molecular Biology are concerned with the use of computing and mathematical sciences as tools to advance traditional laboratory-based biology. With the advent of new automated sequencing and assembly tools, the capabilities to acquire genomic data have become very powerful. This has given rise to an exponential growth of genomic information. The need to process this data for further scientific advances and to understand its role in heredity, chemical processes within the cell, drug discovery, evolutionary studies etc have created new problems that are of interdisciplinary nature. This course will provide an introductory but exciting tour of basic ideas of molecular biology for Computer Scientists and an in-depth look at some of the core algorithms that are used in molecular biology. The students will also learn about computational biology tools available over the Internet.

Pre-requisite: The course is designed for graduate students who might be interested to pursue a possible future research or industry career in bioinformatics. It is also open to senior level undergraduates with good academic standing. There is no formal pre-requisite for the course but having a background in the design and analysis of algorithms will be desirable. A background in biology will be a plus. This course is also open to biology students interested to learn about algorithms and to physics, chemistry, and mathematics and statistics graduate students interested in interdisciplinary research.

Course Outline

A primar on Molecular Biology. Cell. Chromosomes. The structure of DNA. The Central Dogma of Molecular Biology. Gene Expression. Transcription. Types of RNA: mRNA,tRNA and rRNA. Translation. Genetic Code. Mutations. Genomes of prokaryotes, eukaryotes and human.

A brief introduction to data structures and algorithms for Biology students. Exhaustive Search. Greedy algorithm. Divide-and-conquer, Graphs. Trees. Combinatorial pattern matching. Suffix trees.

Mapping and Sequencing. Basic Molecular techniques. Cutting and Pasting of DNA Sequences. Restriction Enzymes. DNA Cloning. Polymerase Chian Reaction. Hybridization. Microarrays. Gel Electrophoresis. Mapping. Physical versus Genetic Mapping. Sequence assembly. Shotgun Assembly. Shortest superstring problem. Sequencing by hybridization.

Sequence Analysis. Measures of sequence similarity. Longest Common Subsequence problem. Dynamic Programming algorithm. Global alignment. Local Alignment. Alignment with gaps. Multiple Sequence Alignment.

Sequence Data Base Search. GenBank. Protein Sequence Database. PubMed. BLAST,BLAST, FASTA, PAM matrices. BLOSUM.

Restriction mapping algorithms. Regulatory motifs in DNA sequence. Motif finding algorithms. Similarity based approach to gene finding problem. repeat finding.

Strings and Evolutionary Trees: Parsinony-based tree building algorithms. Perfect phylogeny problem and algorithms. Distance based methods. Ultrametric trees. Additive distance trees. Connections between multiple alignment and tree construction.

Text

Neil C. Jones and Pavel A. Pevzner, "An Introduction to Bioinformatics Algorithms", 2004, MIT Press, ISBN 0-262-10106-8

Assignments

Homework assignments,reading assignments, a term project, midterm and final examinations.

Webpage

The webpage for this course is http://www.cs.ucf.edu/courses/cap5510/fall2008.This webpage will be used to post most of the course material including lectures, homework assignments, term projects etc. If you click 'Lectures ' below you will get slides and lecture notes. These material are not intended to be complete set of notes which are currently being modified and revised. The material included in these slides and lectures are based on material contained in the text. Many of the slides have been taken directly or adapted from the website associted with the text: http://www.bioalgorithms.info/slides.php. These notes and slides should be used as supplementary material along with live lecture presentation and should only be used as a guide to study the material from the recommended references. Copying for distribution and/or sale is strictly prohibited by copy right laws.