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
Sept 18-20

 

Discuss the HW3 project

 

Python Dictionary’s Regular expressions(ch12)

 

 

Feb 16,18

Knuth-Morris-Pratt Algorithm  also(see Cormen’s Intro to algorithms)

Exam Thur 18

 KMP demo

A nice string matching discussion

Feb 23,25

 Complete KMP

Longest Common Subsequence

 

 HW4:LCS (due Mar 10)

Required Video (quiz next week)

Mar 1,3

Edit Distance

Needleman-­Wunsch
Algorithm (NCBI)

Quiz Mar 8 Tue on video. (forgot to do this)

See UVa 1207

Edit Dist Tutorial

Additional discussion

Mar 8,10

We will select your paper project Tue.

Dr. Halverson lecture on TurnItIn

 TurnItIn Instructions for BioInformatics

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

 suffix array discussion

More suffix arrays

Apr 12,14  BioPython

 Biopython Cookbook

BiopythonHomework(due thur 21)

Apr 19,21

 Multiple Seq Alignment

Clustal Omega

 ClustalW2 download

ClustalW discussion

Neighbor Joining

Apr 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 DFA approach ppt.
  8. Eric Demaine speaks on Tries, suffix trees etc

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