New motif discovery tool - dlocalmotif

[Niall Haslam]

Hi,

new tool from the developers of MEME - allows the use of a negative dataset in addtion to over-representation scoring.

http://bioinf.scmb.uq.edu.au/dlocalmotif/

[Richard Edwards]

I'm sure the MEME guys do it more cleverly but SLiMFinder also has an option to use a negative dataset. :-p Never benchmarked it though. In case anyone wants to try it out, the command is

negatives=FILE : Multiply raw probabilities by under-representation in FILE

Rich

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[Richard Edwards]

If you want to use SLiMFinder to find "local motifs":

http://seqsuite.blogspot.co.uk/2012/11/using-slimfinder-to-discover-local.html