Anaconda (64 bit with python 3.5) Visual studio 17 also has python.
Introduction to Course
Python:Chapters 1 -8 (read before next monday)
|Sep 6||Watch DNA:The secret of Life:E 2||
Python Lists etc
Discuss VS Python.
Python:Chapters 9-11 (read before next monday)
A review of some biology and DNA
NCBI website, FASTA, GENBANK file formats
|HW3:Open Reading Frames (due Sept 29)|
Discuss the HW3 project, regular expressions and dictionaries.
Python Dictionary’s Regular expressions(ch12)
Naive string matching, Rabin-Karp lecture
|nice string matching discussion|
Exam Oct 4
See UVa 1207
Edit Dist Tutorial
|Oct 16,18||Smith-Waterman local alignment, Gaps?, Required Video||
|Oct 16-18||Suffix Tries,Trees ppt|
|Oct 23,25||Wed:Quiz on video ,Suffix Arrays|
|Oct 31 Nov 2||
|SA homework for exam2|
Exam 2 Nov 6
Review python Classes (this weekend add BioPython to your development environment and test it)
BiopythonHomework(due Mon 20)
Multiple Seq Alignment
Exam 3 Thur
|Bring bound printout of the relevant parts of the cookbook.|
|FINAL Week||Comprehensive Final|
Additional Web Resources that I will add to as I find things we might use.
- NCBI website
- Bioinformatics Videos
- Langmead Lab: a wonderful resource of videos and IPython notebooks on DNA sequencing etc.
- Boyer – Moore string searching, Moore’s UT page, short discussion
- Boyer-Moore-Horspool string search algorithm. Short discussion
- Knuth-Morris-Pratt string search algorithm, Robert Sedgewick’s discussion of the full
- Four Russians
- DFA approach ppt.
- Eric Demaine speaks on Tries, suffix trees etc