Bioinformatics Tentative Schedule

Aug 28,30

Python(Severance’s Book)

Watch DNA:The secret of Life:E 1

 Anaconda (64 bit with python 3.5) Visual studio 17 also has python.

Background

Introduction to Course

Python:Chapters 1 -8 (read before next monday)

HW1:Fibonacci (Sept8)

Sep 6  Watch DNA:The secret of Life:E 2

 Python Lists etc

Discuss VS Python.

 HW2:DNA Cutting(sept13)

Python:Chapters 9-11 (read before next monday)

Python Complexites 

Sept 11-13

 A review of some biology and DNA

NCBI website, FASTA, GENBANK file formats

 HW3:Open Reading Frames (due Sept 29)
Sept 18-20

 Discuss the HW3 project, regular expressions and dictionaries.

 

Python Dictionary’s Regular expressions(ch12)

 

Sept 25,27

Naive string matching,  Rabin-Karp lecture

Knuth-Morris-Pratt  lecture,  KMP demo,  ppt

 

nice string matching discussion
Oct 2,4

 

Longest Common Subsequence (demo)

Exam Oct 4

 

 

 

 

Oct 9,11

Edit Distance

Needleman-­Wunsch
Algorithm (NCBI) Compare these two (GI: 1214786271 and GI: 545756033)

 

See UVa 1207

Dot Plots Tutorial (matplotlib)

Edit Dist Tutorial

Additional discussion

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

 suffix array discussion

More suffix arrays

Oct 31 Nov 2

 

Exam Review

SA homework for exam2
Nov 6,8

 Exam 2 Nov 6

Review python Classes (this weekend add BioPython to your development environment and test it)

Nov 12,14

BioPython1

Lets do a zika study(projectZika)

 Biopython Cookbook

BiopythonHomework(due Mon 20)

Nov 19,21

 Multiple Seq Alignment

Clustal Omega

Tree construction (newick format)

 ClustalW2 download

ClustalW discussion

Neighbor Joining

Nov 26,28

 ClustalW

Exam 3 Thur

Bring bound printout of the relevant parts of the cookbook.
May 3,5  Blast
FINAL Week Comprehensive Final 

Additional Web Resources that I will add to as I find things we might use.

  1. NCBI website
  2. Bioinformatics Videos
  3. OpenHelix 
  4. Langmead Lab: a wonderful resource of videos and IPython notebooks on DNA sequencing etc.
  5. Boyer – Moore string searching, Moore’s UT page, short discussion
  6. Boyer-Moore-Horspool string search algorithm. Short discussion
  7. Knuth-Morris-Pratt string search algorithm, Robert Sedgewick’s discussion of the full
  8. Four Russians
  9. DFA approach ppt.
  10. Eric Demaine speaks on Tries, suffix trees etc
  11. NetworkX

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