GENSCAN Information

GENSCAN Information

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How accurate is GENSCAN for human/vertebrate sequences?

How accurate is GENSCAN for invertebrate and plant sequences?

What are some of the limitations of GENSCAN?

How useful are the exon probabilities assigned by GENSCAN?

What are suboptimal exons and what are they good for?

What can be done about repetitive elements?

Other GENSCAN related sites

GENSCAN web server at Pasteur Institute, Paris

GENSCAN web server at DKFZ/EMBnet, Heidelberg

The original GENSCAN web server at Stanford

New York Times article: "Interpreting Your Genes' Instructions"

Report on the NHGRI-Funded Large-Scale Sequencing Meeting, Sep 3 and 4, 1998

Banbury Cross software benchmarking test at CNRS, Marseille

Genesafe gene prediction data set project

GENSCAN email server at MIT .

GENSCAN was developed by Chris Burge in the research group of Samuel Karlin, Department of Mathematics, Stanford University. The program and the model that underlies it are described in:

Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94.

The splice site models used are described in more detail in:

Burge, C. B. (1998) Modeling dependencies in pre-mRNA splicing signals. In Salzberg, S., Searls, D. and Kasif, S., eds. Computational Methods in Molecular Biology, Elsevier Science, Amsterdam, pp. 127-163.

See also:

Burge, C. B. and Karlin, S. (1998) Finding the genes in genomic DNA. Curr. Opin. Struct. Biol. 8, 346-354.

Address any comments/questions/suggestions to: Chris Burge (

Copyright © 1997-2000 Christopher Burge

GENSCAN is freely available for academic use. Executables are currently available for the following Unix platforms: Sun/Solaris, SGI/Irix, DEC/Tru64 and Intel/Linux. Platforms not listed are not currently available. To obtain a copy of Genscan for academic use, do the following:

  1. Go to the academic license agreement web site .
  2. Save the license agreement web page as a text file called 'license.txt' (e.g., if running Netscape use File > Save As... > Text).
  3. Edit the file license.txt to include your name and complete mailing address (not email) using a simple text editor such as SimpleText, emacs, vi, jot, etc. (if you must use Word or WordPerfect, please save the resulting file as ASCII text).
  4. Send the edited license.txt file by email to Chris Burge ( In your email please specify which platform you intend to run Genscan on (Sun, SGI, DEC or Intel/Linux) - I cannot process requests without this information.
  5. Wait for a couple of days to receive the Genscan distribution by email. You should receive a response within one week except during holidays - if you do not, please resend the license.txt file.
For commercial use, contact Imelda Oropeza at the Stanford University Office of Technology Licensing.