Handout #1: Course Information
Durbin chapters 1, 2, 3, 4, 6, (7-8), (9-10).
Gusfield chapters 11, 12, 14, (5-7), (13), (17).
Lecture: Required, TTh 3:00-4:15PM, S360, Clark Center
Discussion Sections: Fridays 4.30-5.30 pm, S360 Clark Center
Useful Information and Handouts
- Teaching Staff
- Old Course Materials (Spring 2003)
- Course Materials for the current offering (Winter 2004)
Genomics is a new and very active application area of computer science.
The past ten years there has been an explosion of genomics data -- the
entire DNA sequences of several organisms, including human, are now
available. These are long strings of base pairs (A,C,G,T) containing all
the information necessary for an organism's development and life. Computer
science is playing a central role in genomics: from sequencing and assembling
of DNA sequences to analyzing genomes in order to locate genes, repeat
families, similarities between sequences of different organisms, and
several other applications. The area of computational genomics includes
both applications of older methods, and development of novel algorithms
for the analysis of genomic sequences. This course aims to present some of
the most basic and useful algorithms for sequence analysis, together with the
minimal biological background necessary for a computer science student
to appreciate their application to current genomics research.
Sequence alignments, hidden Markov models, multiple alignment algorighms
and heuristics such as Gibbs sampling, and the probabilistic
interpretation of alignments will be covered. Applications of these
tools to sequence analysis will be presented: comparing genomes of
different species, gene finding, gene regulation, whole genome
sequencing and assembly. Whenever possible, examples will be drawn
from the most current developments in genomics research.
CS161, Design and Analysis of Algorithms, or equivalent familiarity with
algorithmic and data structure concepts. Basic knowledge of genetics and
biology is helpful, but not required.
Requirements and Grading
The course will have four challenging problem sets of equal size and
grading weight. These must be handed in at the beginning of class on the
due date, which will usually be two weeks after they are handed
Collaboration is allowed on the homeworks.
Recognizing that students may face unusual circumstances and require some
flexibility in the course of the quarter, each student will have a total of
five free late (calendar) days to use as s/he sees fit. Once these
late days are exhausted, any homework turned in late will be penalized at
the rate of 20% per late day (or fraction thereof). Under no
circumstances will a homework be accepted more than three days after its due
Late homeworks should be turned in to a member of the course staff, or, if
none are available, placed under the door of S266 Clark Center. You must
write the time and date of submission on the assignment. It is an honor
code violation to write down the wrong time.
Students with biological and computational backgrounds are encouraged to
Everyone will be required to scribe (produce lecture notes for) one course
lecture. Lecture notes will be
due one week after the lecture date, and will account for 10% of the final
There will be an easy take-home final.
Collaboration is not allowed on the final.
The homeworks will count for 72% of the grade, and the final will count
Collaboration and Honor Code
Students may discuss and work on problems in groups but must write up
their own solutions. When writing up the solutions, students should write
the names of people with whom they dicussed the assignment. Also, when
writing up the solutions students should not use written notes from group work.
The texts for the course are:
- Durbin, Richard et al. Biological Sequence
Analysis. Cambridge University Press, 1998.
- Gusfield, Dan. Algorithms on Strings, Trees, and
Sequences. Cambridge University Press, 1997.
Neither text is an acceptable substitute for attending lectures!
We strongly encourage students to come to office hours.
Please do not e-mail TAs with grading questions. If you want us to explain
why we took points off, you can talk to us after class or during office
hours. If you want a regrade, please submit a written request and
explanation along with the original homework. These can be submitted
after class or during TA office hours.
The class newsgroup is su.class.cs262. This can be used to form study groups amongst yourselves or for online discussions. You may also post questions
regarding problem sets or other difficulties on the newsgroup. We will try to respond to mails regarding any common difficulties.