MAST is a tool for searching biological sequence databases for sequences that contain one or more of a group of known motifs. A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. Motifs are represented as position-dependent scoring matrices that describe the score of each possible letter at each position in the pattern. Individual motifs may not contain gaps. Patterns with variable-length gaps must be split into two or more separate motifs before being submitted as input to MAST. MAST takes as input a file containing the descriptions of one or more motifs and searches a sequence database that you select for sequences that match the motifs. The motif file can be the output of the MEME motif discovery tool or any file in the appropriate format. MAST outputs an xml file which can then be converted into html or text format. The xml file is designed for machine processing and the html file is designed for human viewing. The text format is available for backwards compatibility though due to design decisions made to optimise the xml for html generation the output for separate scoring mode is not identical and some options were removed. The text format will be unsupported in future releases and so we recommend you migrate any programs reading mast output to the xml format.
Parent program: meme
MEME is a tool for discovering motifs in a group of related DNA or protein sequences. MEME takes as input a group of DNA or protein sequences and outputs as many motifs as requested up to a user-specified statistical confidence threshold. MEME uses statistical modeling techniques to automatically choose the best width, number of occurrences, and description for each motif.