MAST -- Motif Alignment and Search Tool

Motif search tool

• e-mail address
  This is the address where the confirmation message and search results will be sent. Make sure this is a valid e-mail address.
• description
  This will be included in the subject lines of the messages MAST will send you. This field is optional so you may leave it blank if you wish.
• motifs
  This is the name of a file on your computer which contains one or more of motifs which characterize a group of related sequences. This can be the name of a file that contains the results of a MEME analysis, one or more profiles in GCG format, or a motifs from any other source as long as they are in the correct format. You can create a motif file by saving the e-mail message MEME sends you to a file. How you save an e-mail message to a file depends on the e-mail program you use--consult your system manager if you need help. A "browse" button is provided by MAST to help you locate the motif file you wish to use. If you use profiles, the gap opening and extension penalties will be ignored.
• sequence database
  This is the name of the sequence database you wish to search for sequences containing your motifs. You select the database from a pull-down menu of available databases. Make sure that you select the right kind of database for your motifs. MAST can only search protein databases with protein motifs and DNA databases with DNA motifs. MAST will search the database of the same type as the motifs in the motif file.
• brief output format
  Choosing this option will cause MAST to produce briefer output. By default, MAST output includes documentation on how to interpret your results. When you chose brief output format, MAST omits this documentation from the output it sends you.

Clicking on the Start search button causes your motifs to be sent to San Diego Supercomputer Center (SDSC) and used to search the database you selected.

The results of the MAST search are sent to you by e-mail.

No copies of your motifs or search results are saved at SDSC after the results have been sent to you.