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Com S 567 Syllabus

Prerequisites

COM S 208; COM S 330; STAT 341; credit or enrollment in BIOL 315, STAT 430

Textbook

Jones, Pevzner. Introduction to Bioinformatics Algorithms, 1st edition, The MIT Press, 2004. ISBN 978-0262101066

Supplementary book: Cormen, Leiserson, Rivest, Stein. Introduction to Algorithms, 3rd edition, The MIT Press, 2009. ISBN 978-0-262-03384-8.

Objectives

Biology as an information science. Review of algorithms and information processing. Generative models for sequences. String algorithms. Pairwise sequence alignment. Multiple sequence alignment. Searching sequence databases. Genome sequence assembly.

Evaluation

Grading will be based on one midterm exam (in-class), one final exam, homeworks, and one project. Grades will be on the following scales:

Homeworks Project Midterm Final
20% 10% 30% 40%

tentative grading scale is as follows.

at least 85                           A
at least 80 but less than 85    A-
at least 75 but less than 80    B+
at least 70 but less than 75    B
at least 65 but less than 70    B-
at least 60 but less than 65    C+
at least 55 but less than 60    C
at least 50 but less than 55    C-
at least 45 but less than 50    D+
at least 42 but less than 45    D
at least 39 but less than 42    D-
below 39                                 F

Assignments

Homeworks will be assigned through blackboard. The assignment will usually be on Thursdays, and the due date will be on Tuesdays before class.

Late submission will be accepted up until 5:00 pm of the due date for a penalty of 25% . No submission will be accepted after that time.

Exams

There will be a midterm exam and a final exam .

There will be a one week window of appeal for each exam beginning the day the exam is returned to the students during recitations. An exam appeal must be in writing and provide information to include the number of the question under issue and a brief statement giving the reason for the appeal. This written statement and the original exam must be given to the instructor during the specified appeal period. The whole exams will be regraded.

There will be no curving or adjustment of everyone's scores on any individual exam. Any curving will be done at the discretion of the instructor at the end of the semester, based on the distribution of overall scores.

Office Hours

Office hours are provided to answer any questions that you may have regarding lecture material, exams or homework. Please take advantage of this opportunity.

E-mail

If you have questions with short answers or you cannot attend any of the office hours, alternatively, you can e-mail oeulenst@cs.iastate.edu, or npappas@cs.iastate.edu.

Disabilities for Special Accommodations

If you have a documented disability and anticipate needing accommodations in this course, please make arrangements to meet with me soon. Please request that a Disability Resources staff send a SAAR (Student Academic Accommodation Request) form verifying your disability and specifying the accommodation you will need.

Academic Honesty

In this course, you may discuss assignments with other students. (Do not assume this is true in all your courses!) We expect you to think through and fully understand assignment solutions. Thus, the solutions you turn in must be written based on your own understanding. Plagiarism will be dealt with harshly. You should consult the University Policy for details regarding academic misconduct and its consequences.