2. Fast Categorization of Bacteriophage Protein Families using Computer Graphics

3. The Problem  We are assembling Protein Families  SAM (Sequence Alignment and Modeling) tells us that sequences are related, but there are times when the program is incorrect, and just by looking at a picture, we can tell it’s wrong, or vice versa.  Therefore, we need a program to let a Human make the comparison on whether certain proteins are homologous or not.

4. Some Background Information  Bacteriophages(phages) are viruses that feed on bacteria to multiply.  Phages are made of proteins, and are some of the quickest way to multiply proteins  Terminase is the family of proteins in phages, whose purpose is the injection of DNA into the bacteria cell.

5. Manually Generated Terminase Graph

6. Computer Generated Terminase Family Graph  Link to Terminase in full size Link to Terminase in full size Link to Terminase in full size  Right half of Terminase in both Diagrams  More accurate than manually generated graph

7. Tree of Programs

8. SS2 Files  SS2 Files, or Secondary Structure 2 Files, is a standard format.  For our current tests, we used ss2 files generated by Psi-pred, although there are others available.  Psi-pred is one of the most reliable available Secondary Structure Prediction Programs

9. A2M Files  A2m files(Alignment to Model) are produced by SAM(Sequence Alignment and Modeling program)  SAM requires a supercomputer to run, therefore, it is not as commonly used as other programs

10. MCALC and CALC  MCALC and CALC serve as a converter between the Secondary Structure prediction program and Gbrowse.  Gbrowse is our free graphics browser, adapted from it’s normal purpose of displaying genes to display proteins.  Gbrowse is short for Genome Browser.

11. Applications  Possible applications of this program include, but not limited to:  Comparing different secondary structure prediction programs to each other  Comparing different settings on SAM in an effort to include everything related to a given Family.  Testing the reliability of SAM, and Psipred.

12. Example Application

13. Q & A  Any Questions?

14. Acknowledgements  I’d like to thank Dr. Hardies and Mandy for letting me intrude in their lab, and either giving me emotional support and help when I needed it.