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Bioinformatics (BINF 400/CHEM 434)

(updated 11/27/12)

Lecture Title	Date	Online	Download	Reading	Workshop	Homework	References
Introduction to course	09/20/12	Intro to Bioinformatics	Intro to Bioinformatics	Intro and Ch. 1 Bioinformatics Text	Workshop#1	Homework#1	References for Lect#1
Sliding windows, dot plots	09/25/12	SlidingWindow	SlidingWindow	Ch. 5 Bioinformatics Text	Workshop#2	Homework#2	References for Lect#2
Programming-Types and operations	09/27/12	PythonLecture1	PythonLecture1	Ch. 13 Bioinformatics Text (Ref: Ch 1-4 BP)	Workshop#1P
Information Organization	10/02/12	Information organization	Information organization	Ch. 2 Bioinformatics Text	Workshop#3	Homework#3	References for Lect#4
Protein Diversity	10/04/12	Protein Div/Glob Align	Protein Div/Glob Align	Ch. 3 Bioinformatics Text	Workshop#4	Homework#4	References for Lect#5
Python programming-if tests, while and for loops	10/09/12	PythonLecture2	PythonLecture2	Ch. 13 Bioinformatics Text (Ref: Ch 5 BP)	Workshop#2P	Homework#1P
Scoring matrices	10/11/12	Protein Div/Glob AlignScoring Matrices	Protein Div/Glob AlignScoring Matrices	Ch. 4 Bioinformatics Text	Workshop#5	Homework#5	References for Lect#6
Sequence alignment	10/16/12	N-W alignment	N-W alignment	Ch. 5 Bioinformatics Text	Workshop#6	Homework#6	References for Lect#7
Introduction to Python - Part II (con't)	10/18/12			Ch. 13 Bioinformatics Text
Introduction to Python - Part III	10/23/12	PythonFile I/O	PythonFileI/O	Ch. 13 Bioinformatics Text	Workshop#3P	Homework#2P
BLAST and PSI-BLAST	10/25/12	BLAST	BLAST	Ch. 6 Bioinformatics Text	Workshop#7	Homework#7	References for Lect#8
Python Programming-functions and debugging	10/30/12	PythonLecture3	PythonLecture3	Ch. 14 Bioinformatics Text (Ref:Ch 6, 10-11 BP)
Multiple Sequence Alignment	11/01/12	MultipleSeqAlign	MultipleSeqAlign	Ch. 6 Bioinformatics Text	Workshop#8	Homework#8	References for Lect#9
Developing Sequence Alignment Algorithms (LCS)	11/06/12	Longest Common Subsequence Alg	Longest Common Subsequence Alg	Ch. 14 Bioinformatics Text	Workshop#4P	Homework#3P
Developing Sequence Alignment Algorithms (Extending LCS to Global and Local Alignment)	11/08/12	Sequence Align Alg	Sequence Align Alg	Project Help		Final Project Assignment
Affine gap penalties	11/13/12	Sequence Align Alg	Sequence Align Alg	Project Help
Protein structure prediction	11/15/12
Programming project help	11/20/12	MSA_ProteinStructurePred	MSAProteinStructurePred	Ch's, 6-7 Bioinformatics Text
Molecular viewers and structure prediction	11/27/12	MolecularViewers	MolecularViewers	Ch. 7 Bioinformatics Text	Workshop#11
Programming Workshop/Course Summary	11/29/12	Course Summary/Programming Workshop	Course Summary	Project help
Final Presentations	12/04/12	Final project presentation and demonstration
EXTRA LECTURES
Information Organization	5/05/09	Information organization	Information organization	Ch. 2 Online Manual	Workshop#7	Homework#7	References for Lect#7
Molecular viewers and tertiary structure prediction	5/28/09	MolecularViewers&Tertiary Structure Prediction	MolecularViewers&Tertiary Structure Prediction		Workshop#10		References for Lect#10
Phylogenetic Analysis		PhylogeneticAnalysis	PhylogeneticAnalysis
Global and Local Alignment	4/19/11	Global and Local Align	Global and Local Align	Ch. 5 Online Manual	Workshop#4	Homework#4	References for Lect#4
Scoring Matrices	4/23/09	Scoring Matrices	Scoring Matrices	Ch. 4  Online Manual	Workshop#5	Homework#5	References for Lect#5
Overview of  Sequence searching		OverviewOf SeqSearch	OverviewOf SeqSearch				References for Lect#11

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