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|
Discuss the HW3 project
Python Dictionary’s Regular expressions(ch12)
Knuth-Morris-Pratt Algorithm also(see Cormen’s Intro to algorithms)
Exam Thur 18
Longest Common Subsequence
HW4:LCS (due Mar 10)
Required Video (quiz next week)
Quiz Mar 8 Tue on video. (forgot to do this)
See UVa 1207
Edit Dist Tutorial
We will select your paper project Tue.
Dr. Halverson lecture on TurnItIn
Antoinette has the specification for the paper as per my email.
|Mar 15,17||Exam 2 Thursday|
|Mar 22,24||Spring Break|
|Mar 31||Paper discussion, Python Classes|
|Apr 5,7||Suffix tries, Trees, Suffix Arrays|
BiopythonHomework(due thur 21)
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 DFA approach ppt.
- Eric Demaine speaks on Tries, suffix trees etc