This is the online version of the p-value computation described in:

Nagarajan N., Jones N. and Keich U. Computing the p-value of the information content from an alignment of multiple sequences Bioinformatics. 2005 Jun 1;21 Suppl 1:i311-i318.

If you use this program in your research, please cite the above paper.

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Direct Computation
You can use this form to directly enter parameter values:

n (Number of sequences) A (Alphabet) DNA L (Length of alignment) s (Entropy score) M (Lattice size)

Background frequencies b1 (Frequency of A's) b2 (Frequency of T's) b3 (Frequency of G's) b4 (Frequency of C's)

Or use this form to upload a file of parameter values in the format "n L s M b1 b2 b3 b4" as in this sample file:

Parameter file:

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MEME/Consensus Input
You can use this form to upload a report from the MEME or the Consensus tool. The report should be from the command-line tool, not the website. In particular, we are expecting plain text input. These files should give you an idea of the format:
MEME report, Consensus report

M (Lattice size) Report file:

MEME Consensus

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For questions and suggestions contact: niranjan at cs.cornell.edu