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MEMERunner

Finds enriched motifs from the given set of DNA sequences. This component is a wrapper for Multiple Em for Motif Elicitation (MEME).

Version 1.2
Bundle microarray
Categories Sequence Motif
Authors Marko Laakso (Marko.Laakso@Helsinki.FI)
Issue tracker View/Report issues
Requires MEME
Source files component.xml MEMERunner.java
Usage Example with default values

Inputs

Name Type Mandatory Description
sequences FASTA Mandatory A list of input sequencies

Outputs

Name Type Description
motifs MotifSet A set of motifs that were found
annot AnnotationTable Motif annotations provided by MEME.
report TextFile MEME output document

Parameters

Name Type Default Description
cpu int 1 Number of parallel processors to be used
instDir string (no default) MEME installation folder
maxw int 15 Maximum motif width
minw int 4 Minumum motif width
nmotifs int 3 Maximum number of motifs to find
pal boolean false Force palindromes
revcomp boolean false Allow sites also on the reverse complement strand

Test cases

Test case Parameters IN
sequences
OUT
motifs
OUT
annot
OUT
report
case1 properties sequences motifs annot (missing)

instDir=/opt/meme,
minw=6,
maxw=8


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