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:
<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 preventMCAST
from 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.