CMSC858W: Algorithms for Biosequence Analysis (Spring 2010)
Time: Tuesday & Thursday, 3:30-4:45pm
Pop (mpop at umiacs) x5-7245
Office hours: TBA
address: 3120F Biomolecular
Sciences Building (bldg #296).
Building is usually locked.
Call me from the intercom and I'll buzz you in.
3223 AVW (by
Qualifier status: counts as a PhD and MS
qualifying course in the Algorithms/Theory area.
This course covers a range of string matching/sequence alignment
topics with a focus on biological applications. In addition to a
survey of several classical algorithms in string matching and
alignment, a major focus will be placed on recent advances in this
field, including space-efficient indices (e.g. extensions of the
Burrows-Wheeler transform) and parallel string-matching algorithms.
While the focus of the course is on biological applications, the
algorithms and techniques described in the course have broader
application in other areas of CS (including NLP, software
engineering, and security).
This course is intended for graduate students with a strong
background in algorithms and data-structures. Programming expertise
is a must. No background in biology is required. If you are uncertain
about meeting these requirements please contact me.
There are no required textbooks for this course. Some of the
material covered can be found in the following two books. In
addition, we will rely on scientific articles describing recent
advances in the field.
on strings, trees, and sequences.
Durbin, Eddy, Krogh,
The course will cover the following main areas.
Introduction to molecular biology
Genome assembly: a
(if time allows) Clustering and phylogenetic analysis
Coursework and grading
Regular homework assignments will consist of a combination of one
or more of the following: (i) exercises from one of the textbooks;
(ii) small programming assignments; (iii) "discovery"
exercises using publicly available bioinformatics tools. In addition,
all students must complete a programming project, chosen by the
students in consultation with the instructor.
The final grades
will be a combination of the grades for the homework, project, and
mid-term and final exams. In addition, participation in the class
will be taken into account for extra credit. The breakdown of you
final grade is shown below.
Homework - 10 %
Project - 30
Midterm - 25%
Final - 35%
late will be graded as follows: up to 1 day late - 10 points will
be deducted from the grade, up to 2 days late - 20 points will be
deducted. Your assignment will not be graded beyond the second day
past the deadline. If for reasons outside your control you will not
be able to submit an assignment on time, see me as soon as
possible to discuss an alternate deadline.
This course follows the University's
attendance policy. In short, if you will miss class for any
reason you should let me know in advance, unless this is not possible
(e.g. sudden illness). In any case, please let me know as soon as you
are aware that will not be able to attend a class (e-mail is OK). I
will work with you to help you catch up on homework or exams if you
have to miss any of the lectures.
I expect that the students taking this class fully adhere to the
Code of Academic
Integrity. Please read this document in full if you have not
already done so. In addition, the University suggests that you sign
the Honor Pledge on every examination you turn in. Please read the
relevant excerpt from the Code of Academic Integrity (reproduced
On every examination, paper
or other academic exercise not specifically exempted by the
instructor, the student shall write by hand and sign the following
I pledge on my honor that
I have not given or received any unauthorized assistance on this
Failure to sign the pledge is
not an honors offense, but neither is it a defense in case of
violation of this Code. Students who do not sign the pledge will be
given the opportunity to do so. Refusal to sign must be explained to
the instructor. Signing or non-signing of the pledge will not be
considered in grading or judicial procedures. Material submitted
electronically should contain the pledge; submission implies signing
On examinations, no
assistance is authorized unless given by or expressly allowed by the
instructor. On other assignments, the pledge means that the
assignment has been done without academic dishonesty, as defined
The pledge is a reminder that
at the University of Maryland students carry primary responsibility
for academic integrity because the meaningfulness of their degrees
depends on it. Faculty is urged to emphasize the importance of
academic honesty and of the pledge as its symbol. Reference on
syllabuses to the pledge and to this Code, including where it can be
found on the Internet and in the Undergraduate Catalog, is