Category
Generic
Usage
ameme good=goodIn.fa [bad=badIn.fa] [numMotifs=2] [background=m1] [maxOcc=2] [motifOutput=fileName] [html=output.html] [gif=output.gif] [rcToo=on] [controlRun=on] [startScanLimit=20] [outputLogo] [constrainer=1]
Manual
This tool is part of UCSC Genome Browser's utilities.
where goodIn.fa is a multi-sequence fa file containing instances
of the motif you want to find, badIn.fa is a file containing similar
sequences but lacking the motif, numMotifs is the number of motifs
to scan for, background is m0,m1, or m2 for various levels of Markov
models, maxOcc is the maximum occurrences of the motif you
expect to find in a single sequence and motifOutput is the name
of a file to store just the motifs in. rcToo=on searches both strands.
If you include controlRun=on in the command line, a random set of
sequences will be generated that match your foreground data set in size,
and your background data set in nucleotide probabilities. The program
will then look for motifs in this random set. If the scores you get in a
real run are about the same as those you get in a control run, then the motifs
Improbizer has found are probably not significant.
Share your experience or ask a question