FAST-MAP

The FAST-MAP beta release ran from July 1, 1996 to July 31, 1997. In that year, our group alone ran roughly 500 contributed gels. The successes were many, including over 150 Pharmacia gels accurately scored within a two week period, and fully automated scoring of ABI/XL gels.

To support and extend this unique intelligent software beyond its limited academic life, the developers have initiated the TrueAllele(TM) Technology. The idea is to pass a ten-fold cost savings in allele calling on to the knowledgeable genetics community.

This CMU site will no longer be supported.

Please visit the new Cybergenetics site for more information. If you have any questions, please send email to perlin@cs.cmu.edu.

Thank you,
Mark W. Perlin, Ph.D., M.D., Ph.D.
Chief Executive Officer, Cybergenetics, Inc.

Welcome to the FAST-MAP website of the Genome Group in the School of Computer Science at Carnegie Mellon University.

FAST-MAP is a pattern recognition computer program that largely eliminates the key bottleneck currently precluding fully automated genotyping of microsatellite markers -- scoring the alleles. Genetic analysis is useful for localizing genes, diagnosing disease, monitoring cancer, identifying individuals, and assessing genetic risk.

The FAST-MAP software is in its preliminary beta release phase, and should not yet be used for automated genotyping. The FAST-MAP software at this site will be updated frequently, as testing and refinement with our beta testers proceeds. Please check weekly for new releases (use the date of the README file to monitor updates).

Note that use of FAST-MAP or any other software that incorporates the TrueAllele(tm) Technology is protected by U.S. patents, and requires a licence from Cybergenetics. For a demo version of the TrueAllele(tm) Technology, please contact Cybergenetics.

Thank you,
Mark W. Perlin, Ph.D., M.D., Ph.D.
Chief Executive Officer, Cybergenetics, Inc.

• Analyzing studies
• Viewing families
• Running FAST-MAP on a Macintosh
• Creating "layout" from ABI sample files
• New programs :
  • setup
  • prep_call
  • prep_view
  • marker_view
  • add_pedigrees
  • display
• Old programs with new names
• Obsolete programs
• Improved interface
• Changed user file formats
• Pharmacia Data

• general
• directory set-up
• updating user files
• generating error messages
• prep_call
• prep_view
• image_call
• image_view
• marker_view
• allele_call
• allele_view
• allele_results

• useful debugging tricks
• recommended protocols

• Matlab tutorial (download postscript)
• Emacs tutorial
• Unix tutorial

And here are some FAST-MAP related websites:

• Matlab
• Perkin-Elmer
• ABI
• ABI GeneScan Sizing and Quantitation Reagents
• Research Genetics

• Ng, S.-K., Mukhopadhyay, N., Rayman, J., Ghosh, S., and Perlin, M. W. (1996) "Fully Automated Microsatellite Genotyping: Computer Software (Abstract)", in American Journal of Human Genetics, 59(4 Supplement): A229.
• Perlin, M.W., Lancia, G., and Ng, S.-K. (1995) "Toward Fully Automated Genotyping: Genotyping Microsatellite Markers by Deconvolution", in American Journal of Human Genetics, 57(5):1199-1210.
• Ng, S.-K., Lancia, G., and Perlin, M.W. (1995) "Toward fully automated genotyping of microsatellite markers by deconvolution (GMBD)", in American Journal of Human Genetics, 57(4 Supplement): A198.
• Richards, D.R., and Perlin, M.W. (1995) "Quantitative analysis of gel electrophoresis data for automated genotyping applications (Abstract)", in American Journal of Human Genetics, 57(4 Supplement): A26.
• Tibbetts, C. (1995) Raw Data File Formats, and the Digital and Analog Raw Data Streams of the ABI PRISM 377 DNA Sequencer.
• Perlin, M.W., Burks, M.B., Hoop, R.C., and Hoffman, E.P. (1994). "Toward fully automated genotyping: allele assignment, pedigree construction, phase determination, and recombination detection in Duchenne muscular dystrophy.", in American Journal of Human Genetics, 55(4): 777-787.

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If you have any questions or comments, please contact skng@cs.cmu.edu