CSC 448: Bioinformatics Algorithms
Fall 2012

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

Office Hours:

When		Who	Where
Tuesday	3:10pm - 4:00pm	Alex	14-215
Wednsday	9:10am - 12:00pm	Alex	14-215
Thursday	3:10am - 4:00pm	Alex	14-215

Additional appoinments: send email.

Final Exam Date: Tuesday,June 5, 2011, 1:10--3:00pm

News and Notes

• The GFF files for 3L are now available here.
  [May 3, 2012]

• The GFF files for Lab 2-2 are available here as a single zip file. You can look at a sample GFF file.
  [April 4, 2012]

• Welcome to CSC 448! Some early announcements are below.
• March 29, 2012 (Thursday): joint lecture with CHEM 441 on Bioinformatics resources and databases. Location: 053 -0201 (Science North). This will be followed by a joint lab with CHEM 441.

• April 10, 2012 (Tuesday): I will be out of town. Aldrin Montana will cover the lecture and supervise the lab on that day.

Old News and Notes

Course Materials

Labs

Lab 0	Meet CHEM 441 students	Due: March 27	Postscript	PDF	[March 25, 2012]
Lab 0 (CHEM 441 handout)	Meet CSC 448 students	Due: March 27	Postscript	PDF	[March 25, 2012]
Lab 2-1	GC-content	Due: April 3/April 5	Postscript	PDF	[April 3, 2012]
Lab 2-2	DNA Analysis (Codon Bias)	Due: April 12	Postscript	PDF	[April 4, 2012]
Lab 3-1	String Matching	Due: April 24 April 26	Postscript	PDF	[April 17, 2012]
Lab 3-2	String Matching	Due: May 10	Postscript	PDF	[April 24, 2012]
Lab 4	Alignment	Due: May 22	Postscript	PDF	[May 15, 2012]
Lab 5	Poster	Due: May 22	Postscript	PDF	[May 23, 2012]

Homework

Homework 1	Midterm Prep	Due: April 26	Postscript	PDF	[April 23, 2012]
Homework 2	Midterm Prep	Due: June 5	Postscript	PDF	[May 28, 2012]

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 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]