CompSci 260: Introduction to Computational Genomics


A computational perspective on the exploration and analysis of genomic and genome-scale information. Provides an integrated introduction to genome biology, algorithm design and analysis, and probabilistic and statistical modeling. Topics include genome sequencing, genome sequence assembly, local and global sequence alignment, sequence database search, gene and motif finding, phylogenetic tree building, and gene expression analysis. Methods include dynamic programming, indexing and hashing, hidden Markov models, and elementary machine learning. Development of practical experience with handling, analyzing, and visualizing genomic data using the scripting language Perl.

The course will require students to program in Perl. Students coming in to the course should know how to program in some computer language, but it need not be Perl. Students should also have had some exposure to basic probability, statistics, and molecular or cellular biology; however, the course has no formal course prerequisites, and significant background will be provided. Please speak to the instructor if you are unsure about your background. This course is a valid elective in both biology and computer science.


Professor Alex Hartemink

Email: amink at
Office Location: LSRC D239
Office Phone: (919) 660-6514

Office hours

Alex Hartemink, Instructor

Email: amink at
Office Hours: Thursday 11:30AM–12:30PM (after class), in LSRC D239 [but not on 18 October]; and also by appointment.

Abrita Chakravarty, TA

Email: abrita at
Office Hours: Monday 11:00AM–12:00PM and Wednesday 12:30–1:30PM, in LSRC D301.

Kenneth Hoehn, UTA

Email: kenneth.hoehn at
Office Hours: Monday 6:00–8:00PM, in the Link (map).

Nikhil Saxena, UTA

Email: nikhil.saxena at
Office Hours: Tuesday 7:00–9:00PM, in the Link (map).

If these office hours do not work for you, please post questions via Piazza, or send any of us an email to schedule an alternate time.


The class meets on Tuesdays and Thursdays 10:05–11:20AM in 116 Old Chemistry (on the Main West Quad, near Bostock Library).