Welcome to the CSULA Bioinformatics Homepage

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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