GIMSAN (by Patrick Ng and Uri Keich of Cornell University) is a DNA motif-finder equipped with a practical and reliable statistical significance analysis. For more details about GIMSAN, please visit the GIMSAN homepage. If you use this program in your research, please cite:

Patrick Ng, Uri Keich. GIMSAN: A Gibbs motif finder with significance analysis. Bioinformatics, 24 (19): 2256-2257, 2008.

GIMSAN is based upon work supported by the National Science Foundation under Grant No. 0644136.

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You will need to upload your input FASTA file (DNA only!) and select (optionally) the genomic file. You will then need to specify the set of width parameters, the size of the nullset which will be used to calculate the P-values, program options, and the number of processors you want the job to run on. A more detailed description of input options is available here.

Calculations will be carried out on the BioHPC compute cluster at CBSU. You will receive e-mail notifications when the job is submitted, when it starts, and when it is finished. Output will be available via links embedded in the notification e-mails. For more information about this program and BioHPC interface in general, please visit our Frequently Asked Questions page.

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E-mail:   (only guests need to use this field, registered users should log in)

Job name:    (please, no spaces, special characters etc., underscore is OK)

Upload your input FASTA file

Estimate background model from

your own genomic file (recommended)
one of our standard genomic files	S288 S. cerevisiae entire genomic contentS288 S. cerevisiae intergenic contentH. Sapiens chr1 intergenic content
input FASTA file

Width parameters (comma-separated list of integers)

Size of the null set

Program options

Zero/one occurences per sequence   -zoops
Single-process time/cycles limit -cput (seconds) -t (cycles)	Rapid convergence rate -L
Consider double strand   -ds	Order of Markov background -markov 0 1 2 3 4 5

Your job will use the number of processors specified below. Increasing this number will lead to shorter execution time, but the job may have to wait longer in queue before it starts. Decreasing the number of processors may cause the job to run too slow and end prematurely if the time limit of 24 hours is exceeded (click on the link below for the most current timeout info). As a rule of thumb, you should add (subtract) one processor for each added (removed) width parameter.
Number of processors

Cluster: This application can't run at this time - no suitable clusters
or you are not authorized to use the service.
The service is available only to Cornell students, faculty, and staff.   ( Show timeout info )