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v1.2 10.05.06
Harvard Medical School Shield Harvard Medical School

NOTE: Due to system-wide upgrade maintenance, the website is currently unavaialble for new analyses
Update: Wednesday, Jan 30, 2019
We're really sorry for the extended downtime of the server. Maintenance work is taking much longer than anticipated. We do not have a definite time horizon at this time, but we are actively working on bringing the site up in a new environment. Please check back every few days.
Help job name:
Help foreground data set (data set from which you wish to extract your motifs)
upload a file:


paste your
data set:

Help foreground
FASTA pre-aligned text
MS/MS Extend From:

Basic options

Help central character
Help width
Help occurrences
Help significance
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        Advanced options

Help upload background
Help background
Help if background is MS/MS generated, extend from?
Help background central character



Please note:
Periodic maintenance of the HMS computer cluster can cause problems with this website beyond our control. Please notify us (by emailing mchou(at) if you do experience problems as we are not always aware of them.

By clicking the 'get motifs' button, you certify that you meet the requirements specified by the following disclaimer: The software provided on this website may be used freely by users from academic and non-profit organizations. Users from the commercial sector should contact Daniel Schwartz (daniel.schwartz(at)

website created by Michael Chou and Daniel Schwartz (Church Lab)
© 2005-2008 The President and Fellows of Harvard College.