Welcome to CSULA Bioinformatics Homepage

Bioinformatics
(Chemistry 434)

(updated 05/28/08)

Lecture Title Date Online Download Reading Workshop Homework References
Introduction to course  3/25/08  Intro to Bioinformatics Intro to Bioinformatics  Ch. 1 Online Manual  Workshop#1  Homework#1 References for Lect#1 
Literature databases  3/27/08 

Literature DBs

Literature DBs

   Workshop#2 Homework#2

References
for Lect#2
Sliding windows, Dot plots 4/01/08 SlidingWindow SlidingWindow Ch. 5 Online Manual Workshop#3 Homework#3  
 Global and Local Alignment 4/03/08 Global and Local Align Global and Local Align Ch. 5 Online Manual Workshop#4 Homework#4 References
for Lect#4
Scoring Matrices 4/08/08 Scoring Matrices Scoring Matrices Ch. 4  Online Manual Workshop#5 Homework#5 References for Lect#5
Introduction to Python - Part I 

4/10/08 

 PythonLecture1 PythonLecture1 Ch 1-4 BP  Workshop#6    
Introduction to Python - Part II

4/15/08

PythonLecture2

PythonLecture2

Ch 5    BP

  Workshop#7  Homework#6  
Introduction to Python - Part II (con't)

4/17/08

 

          
Information Organization 4/22/08

 Information organization

Information organization

Ch. 2 Online Manual

 Workshop#7 Homework#7 References
for Lect#7
BLAST 4/24/08 BLAST BLAST Ch. 6 Online Manual pp 67-72 Workshop#8 Homework#8 References
for Lect#8
PsiBLAST and Multiple Seq Align 4/29/08  PsiBLAST and ClustalW PsiBLAST and ClustalW Ch. 6 Online Manual pp 72-78 Workshop#9 Homework#9 References
for Lect#9
  Introduction to Python - Part III 

 5/01/08 

  PythonLecture3

Ch 6, 10-11  BP

      
Lecture Cancelled 5/06/08            
Python Practice PAM/BLOSUM Workshop and Functions

5/08/08 

           
Developing Sequence Alignment Algorithms  5/13/08  Sequence Align Alg Sequence Align Alg
Pevzner
Smith & Waterman Needleman & Wunsch 

    Final Project
Assignment 		  
Developing Sequence Alignment Algorithms 

5/15/08 

 

  
Pevzner
Smith & Waterman Needleman & Wunsch 		    Final Project
Assignment 		  
Secondary structure prediction  5/20/08  ProteinStructurePred ProteinStructurePred Ch. 7 Online Manual pp 80-87 Workshop#10 Homework#10 References
for Lect#10
Motif searching and molecular viewers 5/22/08 Motif&MolecularViewers Motif&MolecularViewers   Workshop#11   References for Lect#11
Extensions to Global Alignment – Local Alignment, affine gap penalties 5/27/08  AlignmentExtensions AlignmentExtensions Project Help      
Programming Workshop/Course Summary

5/29/08

Course Summary/Programming Workshop

CourseSummary

Project help

 

    
Final Presentations 6/03/08            
EXTRA LECTURES
Phylogenetic Analysis    PhylogeneticAnalysis PhylogeneticAnalysis        
Overview of 
Sequence searching 		   OverviewOf
SeqSearch		 OverviewOf
SeqSearch		       References
for Lect#11
Multiple Sequence Alignment   MultipleSeqAlign MultipleSeqAlign pp 319-351 BFG Workshop#16   References
for Lect#16
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