Massachusetts Institute of Technology


Merck Genome Research Institute


Beth Israel Deaconess Medical Center


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Upper Austria University of Applied Sciences



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News July 2, 2012: The Scan Many Proteins Simultaneously feature has been removed from Scansite due to frequent configuration problems.

October 9, 2009: The Swiss-Prot and TrEMBL databases were updated to their Sept. 22nd 2009 releases. This brings the number of proteins to 509,019 in Swiss-Prot and 9,325,547 in TrEMBL.

NOTE: During heavy usage times, protein domains from Pfam may not be displayed in the Motif Scan graphics, because Pfam allows only one simultaneous request from the same IP address. If this happens, you can retrieve the domains directly from Pfam after finding the motifs in Scansite.

Read about the new features of Scansite 2.0.
The new Scansite 3 is now available at scansite3.mit.edu. Try it!

Motif Scan

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Sequence Match

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Note: Scansite works best with standards-compliant browsers, such as Firefox, Mozilla, Netscape, Opera, Galeon, Safari, and Konqueror. Internet Explorer users may have problems and are encouraged to use an alternative.


Comments or questions? Contact Dr. John Obenauer.