You can create a motif file by saving the e-mail message MEME sends you to a file. If you use profiles, the gap opening and extension penalties will be ignored. 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. Choosing this option will cause MAST to search the nucleotide version of the selected sequence database, converting the nucleotide sequences to protein sequences in all six reading frames. By default, MAST searches the protein version of the selected database when you give it a file of protein motifs. Choosing this option will cause MAST to produce briefer output. By default, MAST output includes documentation on how to interpret your results.