Transcript Fast Categorization of Bacteriophage Protein Families using

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.