GenomeScan

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

GenomeScan incorporates protein homology information when predicting genes. This server allows you to input proteins suspected to be similar to regions of your DNA sequence. You can find such proteins by doing a BLASTX comparison of your sequence to all known proteins, or by running GENSCAN and then comparing the results to known proteins using BLASTP. Please input the proteins in FastA format; the file may contain multiple proteins so long as each is separated by a header on its own line. Files should contain less than one million bases.

If you would like to test the program, feel free to use this DNA testfile and the corresponding protein file.

More information on GenomeScan: GenomeScan homepage

You may also wish to use or read about the GENSCAN server, GenomeScan's predecessor.

Run GenomeScan:

Organism:

Sequence name (optional):

Print options:

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

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

Upload protein(s) with similarity to genomic sequence (FastA format):

Or paste your protein(s) here (FastA format):

GenomeScan was developed by Chris Burge in the Biology Department at MIT. The GenomeScan program and the model that underlies it are described in:

Yeh, R.-F., Lim, L. P. and Burge, C. B. (2001) Computational inference of homologous gene structures in the human genome. Genome Res. 11: 803-816.

GenomeScan is based in part on GENSCAN, described in:

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