Instructor: Alexander Dekhtyar, dekhtyar@calpoly.edu, 14-215
Office Hours:
|
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
Syllabus | Postscript | |||
Piazza Page | HTML | |||
Data Page | HTML | |||
Teams | HTML | |||
UI Code (Java) |
Lab 2-1 | Software Engineering Sprint | Due: April 9 | Postscript | [April 9, 2013] | |
Lab 2-2 | DNA Analysis (Codon Bias) | Due: April 17 | Postscript | [April 11, 2013] | |
Lab 3 | Gene Density | Due: April 29 | Postscript | [April 30, 2013] | |
Lab 4 | Repeats | Due: May 14 | Postscript | [April 30, 2013] | |
Lab 5 | microRNA | Due: May 22 | Postscript | [May 14, 2013] | |
Lab 6 | microRNA | Due: June 3 | Postscript | [May 22, 2013] |
Homework 1 | Midterm Prep | Due: May 9 | Postscript | [April 30, 2013] |
Lecture 0 | March 27 | Bioinformatics in a nutshell | Postscript | [March 26, 2012] | |
Lecture 1 | April 3 | DNA Analysis, Codon Bias, GC Percent | Postscript | [April 3, 2012] | |
Lecture 2 | April 5 | More DNA Analysis | Postscript | [April 4, 2012] | |
Lecture 3 | April 12 | String Matching Algorithms | Postscript | [April 11, 2012] | |
Lecture 4 | April 19 | String Matching: Suffix Trees | Postscript | [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 | [April 18, 2012] | |
Lecture 6 | May 3 | Dynamic Programming (Edit Distance) | Postscript | [May 2, 2012] | |
Lecture 7 | May 8 | Dynamic Programming (Global Alignment) | Postscript | [May 8, 2012] | Lecture 7-1 | May 8 | PAM and BLOSUM matrices | [May 8, 2012] |
Lecture 8 | May 17 | Local Alignment: FASTA | Postscript | [May 17, 2011] | Lecture 9 | May 22 | Local Alignment: BLAST | Postscript | [May 21, 2011] |
Lecture 1 | March 27 | Software Engineering in a nutshell | Postscript | [March 25, 2012] |