Molecular Genetics and Biotechnology Course, spring 2005.

Tentative 2005 course schedule and policies.

Lecture notes:

• Feb. 28; Restriction Enzymes;  Clones.
• These files contain materials removed from the course and retained as reference materials.  These techniques have been mostly surplanted by sequence-based and PCR-based technology.  Restriction mapping by double digestion.   Working with large insert clones.
• Mar. 2; PCR;
• Real Time PCR Screen Shots.
• Mar. 7. Sequencing. Bioinformatics - genome databases.
• Examples of 4 color sequence chromatograms.
• Examining the structure of a human gene.
• Mar. 9. High level expression of recombinant proteins in E. coli.; Saturation Mutagenesis.
• Mar. 14 Site-specific In Vitro Mutagenesis; Bioinformatics of Protein families
• Exploring a protein family through the web

Final exam and key for 2005

Help pages for bioinformatics software.

• Using Entrez at NCBI to find sequences or sets of sequences by description.
• Using Psi-Blast.
• Using PHI-Blast and regular expression searching.
• Help with ssh and scp (or Putty)
• Making X-windows connections.
• Connecting with X-windows.
• Sources of X-window interface software.
• Exporting a desktop to your PC.
• Screen capture from the X-windows display.
• Using VNC viewer instead of an X-windows server
• Screen capture utilities from various platforms.
• Methods to view sequence 4 color traces.
• Methods to predict secondary structure from sequence.
• Comparison of Psi-Blast, ClustalW, HMMER, and SAM capabilities.
• Obtaining cDNA clones.
• Help on linux and the vi editor.
• How to set up your own web page on the biochemistry server.
• Technical instructions .
•  Examples of the use of personal web pages in research applications.
• Dr. Hardies' biotech bookmarks.
• Bioinformatics resources at UTHSCSA.
• Programs maintained by Steve Hardies
• Genomics software (Olig, LaserGene, VectorNTI, GCG, ClustalW, SAM, HMMER, EMBOSS package)
• Installing Vector NTI.
• Using the local Net Blast interface or local standalone Blast suite on bioinf. Includes:
• Synopsis of Blast suite, Psi-Blast, RPS-Blast, BlastClust, Regular expression searching.
• Directions to documentation.
• Description of UTHSCSA mirror of  NCBI databases.
• Local database management tools.
• Link to local NetBlast server.
• GCG (Wisconsin Package).
• Making connections.
• Major functions and alternatives.
• Troubleshooting.
• CLUSTALW
• Local implementation and links to documentation.
• Different versions an implementations.
• Integration of Neighbor Joining and Bootstrap Analysis.
• HMMER  - a profile method for analyzing protein families (local implementation).
• Links to documentation and program status
• Expanding Pfam models.
• Making novel HMMER HMM models.
• Using HMMER as an alignment tool.
• SAM (Sequence Alignment and Modeling System) - A tool for analyzing protein superfamilies, up the the fold recognition level.
• Links to documentation and program status
• Use of the target99 script.
• Assorted SAM programs and utilities.
• The a2m format
• PhredPhrap
• Set-up steps to use the UTHSCSA phred phrap installation
• How to access Phred phrap documentation and run the "quick tour" tutorial.
• Outline of steps to start a new project.
• Structure software. (Insight II).
• Insight II help files.