MEME motif discovery

[Rocky Parida]

Hi
I have a question on meme motif discovery and directionality.
When searching for motifs does MEME considers by default both forward and reverse strands of a given input sequence to generate a motif? I read in it in this https://groups.google.com/forum/#!topic/meme-suite/1bTc2sDBqZU that MEME considers both forward and reverse strand when discovering motif (assuming you were taking about motif discovery and not pattern matching because I can see in patten matching MAST does consider both strands).

Also if the above is true then why does the manual gives an option for -revcomp.
As described in under this option:
when given -revcomp Consider both the given strand and the reverse complement strand when searching for motifs in a complementable alphabet (ie DNA).
by default- Search for motifs of complementable alphabets on the given strand only.

Please clarify.
Rocky

[CharlesEGrant]

Hi Rocky, 

You posted this question twice. I deleted the other copy.

That post was alluding to the MEME web application. The command line and web versions of MEME have slightly different default behavior. The MEME web application tries to use the most commonly used values of the command line parameters. Most users want to consider motif instances on both strands, to the MEME web application calls MEME using the '-revcomp' parameter. You can always see the exact command line used by the web application at the bottom of your results, in the section labeled "Command line". If you are using the MEME web application you can turn off looking at the reverse complement by selecting the "search given strand only" check box in the advanced options section.

[Rocky Parida]

Hi Charles
Based on your answer -revcomp is not set as default by meme command line version but only by the web application version due to common usage.
Thank you very much for the reply.
Rocky