MAST: Motif Annotation Search Tool

MAST is part of the MEME package.

MAST uses the motifs discovered by MEME in a group of related sequences to annotate other sequences. Each sequence in a database of sequences is searched for matches with each of the motifs.

MAST prints:

• a histogram of ZSCORES
• a list of high-scoring sequences sorted by ZSCORE
• motif schematic diagrams for high-scoring sequences
• the high-scoring sequences annotated with most likely motif positions and their scores.

The MAXSUM score for a sequence is the sum of the single maximum score for each motif, regardless of whether it is over the threshold, and regardless of whether it would overlap the maximum-scoring position for another motif. ZSCORES are (MAXSUM - AVG)/SD where AVG and SD are calculated from the dataset being searched using ProfileNormal. Schematic diagrams and annotations are printed only for sequences with ZSCORES at least .

Block diagrams show the order and spacing of *non-overlapping* matches to the motifs in each high-scoring sequence. Motif matches (score >= threshold) are shown in brackets "[]", weak matches (0 <= score < threshold) are shown in angle brackets "<>", and the length of non-motif sequence ("spacer") is shown between dashes "-". For example,

27-[3]-44-<4>-99-[1]-7

shows an initial spacer of length 27, followed by a strong match to motif 3, a spacer of length 44, a strong match to motif 4, and so on.