The GENSCAN Web Server at MIT

Identification of complete gene structures in genomic DNA

For information about Genscan, click here

Server update, November, 2009: We've been recently upgrading the GENSCAN webserver hardware, which resulted in some problems in the output of GENSCAN. We apologize for the inconvenience. These output errors were resolved.

This server provides access to the program Genscan for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms.

This server can accept sequences up to 1 million base pairs (1 Mbp) in length. If you have trouble with the web server or if you have a large number of sequences to process, request a local copy of the program (see instructions at the bottom of this page).

Organism: Suboptimal exon cutoff (optional):

Sequence name (optional):

Print options:

Upload your DNA sequence file (upper or lower case, spaces/numbers ignored):

Or paste your DNA sequence here (upper or lower case, spaces/numbers ignored):

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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.