Is there a way to tell MEME to search for motifs that are similar to a specific (supplied on input) sequence?

[Joel Wallenius]

I looked through the tutorials but couldn't find anything. I saw that you could input motifs and search through databases, but not de-novo discovery based on a 'template'.

Is there something I'm missing, or can it not be done currently?

[CharlesEGrant]

The closest facility would be the '-cons' option in the command line version of MEME. This '-cons' option lets you specify a consensus sequence that MEME will use as a starting point for it's motif search. This option is not available from the web application.

[Joel Wallenius]

OK, that is actually quite close. Have you used it yourself? Will it make MEME blind to motifs that are not similar to this consensus sequence?

Big thanks Charles. You are invaluable!

[CharlesEGrant]

Will it make MEME blind to motifs that are not similar to this consensus sequence?

Blind is too strong a word. It just provides the starting point for MEME search. MEME will still try to optimize the motif,  so if your sequences contained a very strong motif that was spatially adjacent to occurrences of your consensus sequence, MEME might still get pulled away. It is unlikely though.