CSC 448: Bioinformatics Algorithms
Spring 2013

Instructor: Alexander Dekhtyar, dekhtyar@calpoly.edu, 14-215

Office Hours:

When		Who	Where
Monday	1:10pm - 2:00pm	Alex	14-215
Tuesday	2:10pm - 3:00pm	Alex	14-215
Wednsday	9:10am - 12:00pm	Alex	14-215

Additional appoinments: send email.

Final Exam Date: Tuesday, June 11, 2013, 4:10--7:00pm

News and Notes

Old News and Notes

Course Materials

Labs

Lab 2-1	Software Engineering Sprint	Due: April 9	Postscript	PDF	[April 9, 2013]
Lab 2-2	DNA Analysis (Codon Bias)	Due: April 17	Postscript	PDF	[April 11, 2013]
Lab 3	Gene Density	Due: April 29	Postscript	PDF	[April 30, 2013]
Lab 4	Repeats	Due: May 14	Postscript	PDF	[April 30, 2013]
Lab 5	microRNA	Due: May 22	Postscript	PDF	[May 14, 2013]
Lab 6	microRNA	Due: June 3	Postscript	PDF	[May 22, 2013]

Homework

Homework 1

Midterm Prep

Due: May 9

Postscript

PDF

[April 30, 2013]

Lecture Notes

Lecture 0	March 27	Bioinformatics in a nutshell	Postscript	PDF	[March 26, 2012]
Lecture 1	April 3	DNA Analysis, Codon Bias, GC Percent	Postscript	PDF	[April 3, 2012]
Lecture 2	April 5	More DNA Analysis	Postscript	PDF	[April 4, 2012]
Lecture 3	April 12	String Matching Algorithms	Postscript	PDF	[April 11, 2012]
Lecture 4	April 19	String Matching: Suffix Trees	Postscript	PDF	[April 18, 2012]
Lecture 4.5		String Matching: Suffix Trees, Ukkonen's Algorithm		PPTX	[May 16, 2013]
Lecture 5	April 24	Repeated Sequence/Palindrome Detection	Postscript	PDF	[April 18, 2012]
Lecture 6	May 3	Dynamic Programming (Edit Distance)	Postscript	PDF	[May 2, 2012]
Lecture 7	May 8	Dynamic Programming (Global Alignment)	Postscript	PDF	[May 8, 2012]
Lecture 7-1	May 8	PAM and BLOSUM matrices		PDF	[May 8, 2012]
Lecture 8	May 17	Local Alignment: FASTA	Postscript	PDF	[May 17, 2011]
Lecture 9	May 22	Local Alignment: BLAST	Postscript	PDF	[May 21, 2011]

Lecture Notes for CHEM 441

Lecture 1

March 27

Software Engineering in a nutshell

Postscript

PDF

[March 25, 2012]