CSC 448: Bioinformatics Algorithms
Fall 2014

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

Office Hours:
When
Who Where
Monday 9:30pm - 12:00pm Alex 14-215
Tuesday 11:10pm - 12:00pm Alex 14-215
Wednsday 10:10am - 11:00am Alex 14-215

Additional appoinments: send email.

Final Exam Date: Tuesday, December 12, 2014, 4:10--7:00pm

News and Notes

Course Materials

Syllabus Postscript PDF
Piazza Page HTML
Requirements Template DOC
Lab 2-2 GUI code .tar.gz
Data Page HTML

Labs

Lab 1 Meet CHEM 441 students Due: September 24 Postscript PDF [October 2, 2014]
Lab 2-1 Software Engineering Sprint Due: September 30 Postscript PDF [OCtober 2, 2014]
Lab 2-2 DNA Analysis (GC Content) Due: October 8 Postscript PDF [October 2, 2014]
Lab 3 Gene Density Due: October 15 Postscript PDF [October 8, 2014]
Lab 4 Repeats Due: October 30 Postscript PDF [October 16, 2014]
Lab 5 Motif Discovery Due: November 25 Postscript PDF [November 20, 2014]

Homework

Homework 1 Midterm Prep Due: May 9 Postscript PDF [November 4, 2014]

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]

September 19, 2014, dekhtyar at csc.calpoly.edu