CSC 448: Bioinformatics Algorithms
Fall 2015

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

Office Hours:

When		Who	Where
Tuesday	9:10am - 10:00am	Alex	14-215
Wednesday	9:10am - 10:00am 11:10am - 12:00pm	Alex	14-215
Thursday	9:10am - 10:00am	Alex	14-215

Additional appoinments: send email.

Final Exam Date: Thursday, December 10, 2015, 4:10--7:00pm

News and Notes

Course Materials

Labs

Lab 1	Meet CHEM 441 students	Due: September 22		PDF		[September 22, 2015]
Lab -1	DNA Decoder	Due: September 29		PDF	Data	[September 24, 2015]
Lab 2-1	Software Engineering Sprint	Due: September 30	Postscript	PDF		[October 1, 2015]
Lab 2-2	DNA Analysis (GC Content)	Due: October 7	Postscript	PDF	[October 8, 2015]
Lab 3	Gene Density	Due: October 14	Postscript	PDF	[October 8, 2015]
Lab 4	Matching	Due: October 29	Postscript	PDF	[October 15, 2015]

Homework

Lecture Notes

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Lecture 0		Bioinformatics in a nutshell	Postscript	PDF		[September 19, 2014]
Lecture 1		DNA Analysis, Codon Bias, GC Percent	Postscript	PDF		[September 19, 2014]
Lecture 2		More DNA Analysis	Postscript	PDF		[September 19, 2014]
Lecture 3		String Matching Algorithms	Postscript	PDF		[September 19, 2014]
Lecture 4		String Matching: Suffix Trees	Postscript	PDF	PPTX	[September 19, 2014]
Lecture 5		Repeated Sequence/Palindrome Detection	Postscript	PDF		[September 19, 2014]
Lecture 6		Dynamic Programming (Edit Distance)	Postscript	PDF		[September 19, 2014]
Lecture 7		Dynamic Programming (Global Alignment)	Postscript	PDF		[September 19, 2014]
Lecture 8		PAM and BLOSUM matrices		PDF		[September 19, 2014]
Lecture 9		Local Alignment: FASTA	Postscript	PDF		[September 19, 2014]
Lecture 10		Local Alignment: BLAST	Postscript	PDF		[September 19, 2014]
Lecture 11		Hidden Markov Models	Postscript	PDF		[November 20, 2014]

Lecture Notes for CHEM 441

Lecture 1

Software Engineering in a nutshell

Postscript

PDF

[September 19, 2014]