Create Epitome

"CreateEpitome" is an interactive program (created via Silverlight) and a command-line program for Windows.

Given a weighted set of amino-acid sequences, it creates a new amino-acid sequence that covers input sequences. It works step-by-step, producing an output line after each step. The possible steps include:
To achieve reasonable efficiency, the program

References

D. Yerly, D. Heckerman, T. Allen, T. Suscovich, N. Jojic, C. Kadie, W. Pichler, A. Cerny, C. Brander. Design, expression and processing of epitomized HCV encoded CTL epitopes. J. Immunol, to appear.

D. Nickle, N. Jojic, D. Heckerman, V. Jojic, D. Kirovski, M. Rolland, S. Pond, J. Mullins. Comparison of immunogen designs that optimize peptide coverage: Reply to Fischer et al., PLoS Computational Biology, 4(1):e25, January 2008.

D. Nickle, M. Rolland, M. Jensen, S. Pond, W. Deng, M. Seligman, D. Heckerman, J. Mullins, and N. Jojic. Coping with viral diversity in HIV vaccine design, PLoS Computational Biology, 3(4): e75, April 2007.

N. Jojic, V. Jojic, B. Frey, C. Meek, and D. Heckerman. Using epitomes to model genetic diversity: Rational design of HIV vaccine cocktails. NIPS 2005.

Web Version

http://atom.research.microsoft.com/EpitomeCreator/

Pre-Compiled Programs for Windows

Interactive Version

Command-Line Exe's:

Source Code Files

(To download see Source Code tab above)
Compiling the project requires
Some source code features of possible interest:
How to run regression tests