C.Stuart Baxter

Course description:
 

• the accession, analysis and manipulation of biological information by computational methods
• a course designed primarily for molecular biologists

• an increasingly urgent need currently exists for biologists with experience in this area

1.  Internet-based  resources and databases for genetic and other biological information.

2.  Homology searching for protein and nucleic acid identification: comparison of methods

3.  Essentials of phylogenetic analysis

4.  Computational methods for gene analysis, identification and location

5.  Complete genomes - biological insights from comparative studies

6.  Large scale analysis of gene expression methods

7.  Motif identification in nucleic acid and protein sequences

8.  2-D and 3-D protein structure prediction methods

9.  Metabolic pathway analysis

10. In silico simulation of pathways, cells and experiments
 

REQUIREMENTS:  Curiosity, receptiveness to the information technology revolution

NONREQUIREMENTS:  Computing skills, knowledge of  computer languages,
      more - than - basic mathematics.
 

Computer classroom instruction with hands - on experience involved - sign up soon!
 

Instructor:  C. Stuart Baxter, Ph.D.
   Department of Environmental Health, Room 201
   Tel: 558-1704
   Email: C.Stuart.Baxter@UC.EDU
 

COURSE SCHEDULE

Logistics, Introduction

1:  Pairwise Alignment I.  The Dynamic Programming Algorithm

2:  Pairwise Alignment II.  Homology Searching Algorithms.

3.  Database and Homology Searching

Database searching
BLAST problems   ©
a.  yeast gene amplification problem
b.  BLAST searches with distantly - related proteins
Homology Searching Guides & Resources

4.  Weight Matrices for Sequence Similarity Scoring

5.  BLAST and variants; PHI & PSI BLAST.

6.  Multiple Alignment

7.  Phylogenetic Analysis

8.  Motif Identification

9.  Genomics I - Gene structure prediction and analysis – exon, promoter, splice site identification

10. Genomics II - Whole genome – based analysis methods, COGs

11. Genome-wide Analysis of Gene Transcription

12. Proteomics I

13. Proteomics II

14. Proteomics III

15. Metabolic Pathway Analysis

16. Cell Biology In Silico. Electronic simulation of cells and pathways. Web – based Resources