Topic
|
Date
|
Remarks
|
Introduction: Python
|
01/17/17
|
|
Comparing DNA sequences
|
01/19/17
|
HW 1
|
Sequence alignment
|
01/24/17
|
Alignment notes
HW 1 solution
|
Random traceback to compute random alignments
|
01/26/17
|
HW 2
|
Needleman-Wunsch
|
01/31/17
|
Needleman-Wunsch slides
|
Functions
|
02/02/17
|
HW 3
|
Needleman-Wunsch and runtime analysis, BLOSUM62
|
02/07/17
|
Needleman-Wunsch slides
BLOSUM 62
|
Snow day - classes cancelled
|
02/09/17
|
|
Finding similar sequences in a database - Smith Waterman
|
02/14/17
|
Smith-Waterman alignment
HW 4
Horse Haemoglobin (PDB 2dhb)
Sequences from BLAST search
BLAST output
Global and local alignment scores with BLOSUM_62
Chicken Cytochrome bc 1 (PDB 3h1j)
Sequences from BLAST search
BLAST output
Global and local alignment scores with BLOSUM_62
|
Smith-Waterman
|
02/21/17
|
DNA example input and output for Smith-Waterman alignment
Smith Waterman in Python
|
BLAST-like alignment
|
02/23/17
|
BLAST alignment
E.coli K12 MG1655 genome
Related proteobacteria genomes
Bacterial phylogeny
NWscore alignment function in Python
Programming assignment 1
T-cell antigen receptor (PDB 1TCR)
Sequences from BLAST search
T-cell antigen receptor (PDB 1TCR)
Sequences from BLAST search
|
BLAST-like database search
|
02/28/17
|
|
BLAST-like database search and practice problems
|
03/07/17
|
Practice problems
|
Exam review and makeup class
|
03/08/17
|
|
First exam
|
03/09/17
|
|
Spring break
|
03/14/17
|
|
Spring break
|
03/16/17
|
|
Distance based phylogeny reconstruction
|
03/21/17
|
UPGMA
|
UPGMA algorithm, data structure to represent phylogenies
|
03/23/17
|
UPGMA implementation
Python function to make Newick tree
HW 5
|
UPGMA implementation in Python
|
03/28/17
|
HW 6
|
UPGMA implementation in Python and Newick format
|
03/30/17
|
Jukes Cantor distance matrix for Haemoglobin aligned sequences
Online phylogeny viewer
|
UPGMA in Python
|
04/04/17
|
|
UPGMA in Python
|
04/06/17
|
HW 7
|
Jukes Cantor distance matrices
|
04/11/17
|
|
UPGMA on simulated data
|
04/13/17
|
HW 8
|
Neighbor joining
|
04/18/17
|
|
Additional topics
|
04/20/17
|
|
Second exam review session 2:30 to 3:30 (Room TBA)
|
04/24/17
|
|
Second exam
|
04/25/17
|
|
Additional topics and final review
|
04/27/17
|
|
Final exam, FMH 108 2:30 to 5pm
|
05/11/17
|
|