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

Syllabus Postscript PDF
Piazza Page HTML
Data Page HTML
Teams HTML
UI Code (Java)



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]


March 25, 2012, dekhtyar at csc.calpoly.edu