SpaMo does inference of transcription factor complexes by looking for significant spacings between binding sites. The inputs are a set of many short sequences, a primary motif and one or more databases of secondary motifs. It searches for the strongest primary motif binding site and then searches in the area around it looking for the strongest secondary motif binding site. The relative spacings of the primary and secondary motif in all the sequences is tallied and the probability of the close spacings happening by chance is calculated. After all the calculations are done SpaMo outputs the non-redundant secondary motifs in order of significance provided they had a bin that passed the significance threshold. Similar secondary motifs are grouped together and listed in order of significance on the secondary motif they were redundant to. If the bin size is one then an alignment for each of the similar secondary motifs is created.
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.