mcast

Usage:
mcast [options] <motifs> <database>

Description:

mcast Searches a sequence database for clusters of known motifs. Like beadstring, and miao, this mode employs a motif-based hidden Markov model, but uses a star topology and a novel scoring algorithm. The motifs may appear in any order. A full description of the algorithm is found in:
Bailey and Noble. "Searching for statistically significant regulatory modules." Bioinformatics (Proceedings of the European Conference on Computational Biology). 19(Suppl. 2):ii16-ii25, 2003.

Input:

Output:

An XML file using the CisML schema.

Options: