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. This allows motifs to occur on either strand and still count toward the overall E -value of the match. The results are displayed separately for the two strands, as though both had occurred in the database. This option can improve search selectivity when erroneous matches are due to biased sequence composition . Selecting this option will cause MAST to use a different random model for each target sequence .