Topics in Computational Biology and Genomics

BioE/MCB/PMB c146/c246, Spring 2005

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Homework

Requirement for C246 Sections

Students enrolled in graduate student sections (BioE/MCB/PMB C246) have an additional requirement.

On any FIVE of the problem sets, write a paragraph explaining how the concepts presented in the past week have applications to your own research, or to research projects that you know about. Be specific.

Oral discussion of the class and homework is encouraged. However, all homework questions must be answered in writing alone and must be fully understood. You must also list all the people with whom you discussed the question.

Clear, precise writing and good code style are important. code style example

Problem Set 1 due Monday, 24 January 2005 by 6:00 pm. Bring an identical hard copy at the beginning of lecture on January 25.
- Codon table

Problem Set 2 due Monday, 31 January 2005 by midnight. Bring an identical hard copy at the beginning of lecture on February 1.
- Score matrix for problem 2
- Sequences for problem 5

Problem Set 3 due Monday, 7 February 2005 by midnight. Bring an identical hard copy at the beginning of lecture on February 8.

Problem Set 4 due Monday, 21 February 2005 by midnight. As always, bring an identical hard copy at the beginning of lecture on February 8.

Problem set 5 due Monday, 28 February 2005 by midnight.

Problem set 6 due Tuesday, 8 March 2005 at 11 am. Hand in a paper copy in class as usual. NOTE: Solutions will be available Tuesday evening. Thus, we can not accept late problem sets turned in after 6pm Tuesday.
- sequences for problem 4
- alignment for problem 6
- alignment program if needed. Download and run it as
aligner.pl -m matrixfile -p gap penalty (positive) -a [global | local | noend] -o outputfile seq1.fasta seq2.fasta

Problem set 7 due Monday, 11 April 2005 at midnight.

Solutions