CAP 5510 (Bioinformatics)

Instructor:	Tamer Kahveci
Email:	tkahveci AT ufl DOT edu
Location:	Little Hall, LIT0113
Time:	Monday/Wednesday/Friday (10:40 - 11:30 AM)
Office hour:	Monday/Friday 11:50 AM - 12:40 PM
Contact:	Malachowsky Hall 5400C (office), Email above
TA:	Jingzhou Hu (jingzhouhu @ ufl)

Goals:

This course will discuss the major components of bioinformatics data (such as DNA and protein sequences and protein structures) and how computer technology is used to understand this data better.

Announcements:

Zoom link for office hours in case you cannot make it to my office "https://ufl.zoom.us/my/tkahveci join meeting -> tkahveci (passcode = 231442)
Here are class projects from 2011, 2012, 2013, 2014, 2015, 2016.
You will find course slides here.
You will find the course schedule here. I will update this throughout the semester.
Project proposal description is ready.
Details on project reports are ready.
You will use Canvas to submit soft copies of your homeworks and check grades.
Here is the course syllabus
Check the class page regularly for announcements .

Prerequisites:

I will assume that you have already taken data structures and algorithms courses and you are comfortable with basic computer programming (e.g., with C or Java).

Topics:

I am planning to cover the following topics.

Biological sequences
Lossless alignments (different DP problems such as global, local alignment, etc,)
Protein structures and function (primary, secondary, etc.)
Substitution matrices, statistics
Heuristic alignments (BLAST, etc)
Phylogeny
Multiple sequence alignment
Sequence assembly
Biological networks

Grading:

Grading will be based on homeworks and quizzes (50 %), project (50 %). I will reward high quality projects with up to 2.5 % bonus points.

Text book:

I will teach this course from multiple books and some research papers. Therefore, I do not require any textbook. For interested students, I recommend the following books as resources:

Fundamental Concepts of Bioinformatics by Dan E. Krane, Michael L. Raymer. (ISBN: 0805346333)
Bioinformatics: Sequence and Genome Analysis by David W. Mount. (ISBN: 0879696087)
Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology by Dan Gusfield. (ISBN: 0521585198)
Algorithms in Bioinformatics: A Practical Introduction by Wing-Kin Sung.(ISBN-13: 978-1420070330)

Other:

Check out disability resources.
Cheating, plagiarism, and other types of academic dishonesty will be subject to punishment.
I encourage class attendence.
Please return your assignments in time. Late returns will cause 20 % deduction in your grade for that assignment for each late day. Submissions after 5 days from the due date will not be graded.
Please visit only during office hours. If you really need to meet me out of the office hours email me to make an appointment. If I postpone or cancel the office hour, I will post it in the announcements section and (try to) put a note on my office door.
Please avoid any activities that will disturb the flow of the lectures: Silence your cell phones, pagers, etc.

Tamer Kahveci