mcast [options] <motifs> <database>
Description:
mcastSearches 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:
<motifs> is a list of motifs, in MEME format.
<database> is a collection of sequences in
FASTA format.
Output:
Options:An XML file using the CisML schema.
--bgfile <bfile>- Read background frequencies from<bfile>. The default is to use frequencies embedded in the application from the non-redundant database. If the argument is the keywordmotif-file, then the frequencies will be taken from the motif file.--e-thresh <ev>- Only print results with E-values less than<ev>.--max-gap <max-gap>- The value of<max-gap>specifies the longest distance allowed between two hits in a match. Hits separated by more than<max-gap>will be placed in different matches. Note: Large values of<max-gap>combined with large values of pthresh may preventMCASTfrom computing E-values.--max-seqs- Print results for no more than<max><max>sequences. By default, all matches are reported, up to the specified E-value threshold (see--e-thresh).--motif <id>- Use only the motif identified by<id>. This option may be repeated.--progress <value>- Print to standard error a progress message approximately every<value>seconds.--synth- Create synthetic sequences for estimating E-values. This is useful with small input databases where not enough match scores are found to estimate E-values.--verbosity 1|2|3|4- Set the verbosity of status reports to standard error. The default level is 2.