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Transcript
Fast Categorization of Bacteriophage Protein Families using Computer Graphics 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. 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. Manually Generated Terminase Graph Computer Generated Terminase Family Graph Link to Terminase in full size Right half of Terminase in both Diagrams More accurate than manually generated graph Tree of Programs 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 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 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. 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. Example Application Q&A Any Questions? 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.