MAST looks for sequence orderss for matches to motifs defined, and sorts the sequences by the best combinable match to all motifs.
MAST implies ‘Motif Alignment and Search Tool’. A motif is a sequence scheme that takes place repeatedly in a group of related sequence orders. Motifs are chracterized as position-dependent probability that explain the probability of each possible letter at each position in the scheme. Motifs of individual basis may not obtain gaps. Schemes with variable-length gaps must be united into two or more separate motifs before being released as input to MAST.
MAST gets as input a file having the descriptions of one or more motifs and lokks for a set of sequence orders that you choose for sequences that match the motifs.
MAST is capable to look for sequence orders with motifs of the same alphabet but as a special feature it can also look for protein sequences with DNA motifs. You can manage how (or if) MAST scans the reverse complement strand (if necessary). You can also define thresholds for overall (combined match) importance and individual motif site significance.