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Frequently Asked Questions

How to use the MEME suite ?

0 votes

Dear colleagues,

I have no background in bioinformatics, I don't know how to write a script, I can just use a pipette and do some stuff on the bench, so I would need someone who can help me to find some motif in a genome..

Here is the idea, I am working on 2 t-box genes in Caenorhabditis elegans. It is quite accepted that most of the t-box proteins bind to DNA with almost the same motif. This motif is known, the PWM is known. So I would like to use these elements to scan the entire C.elegans genome.

As output, I would like to have a list of putative binding site, with their positions (if they are in 5' region, intron, 3' region etc etc) and if they could be real or not.

I would like this result to see if already from such analysis we can see some trends in the genome.

I heard that the best tools to make such analysis is the Meme suite, I tried by my own to use it but I always have some errors in everything I try.

So if someone could help me to do this analysis it could be amazing !

Best regards


asked Dec 6, 2014 in NGS data analysis by thomas.daniele (120 points)

So the meme suite has a tool called fimo which you can use to scan the whole c.elegans genome with your motif. to then assign the location of the motif w.r.t the genes you can use the ceas annotate tool in galaxy.
what errors do you get in meme? if you post the error and the inputs you use i might be able to help, eventhough i never used the online version of meme.

Good luck,

2 Answers

+1 vote
Dear Thomas,

in addition to do the anaysis yourself - following Johannas suggesions is certainly a good start - I would also always check if someone has done this already. Nowadays many model organisms have been analysed intensively already, and you might find the predicted binding sites for C. elegans in public databases. With this you do not run into all the problems associated with the seamingly simple task of scanning a motif genome wide (many false positives will occur). And you can cite somebody as a reference.

In principle, the original "MEME" tool does "de-novo motif discovery" from a set of sequences - this is different to a "motif search", where the PWM is known (as in your case). The latter is done with FIMO for example. Whether the found match is "real" or not can only be decided experimentally in thw wet-lab. But you get statistical information, if at least the match is unlikely to occur randomly. The matching positions are usually reported by many tools, but such detailed information of promoter, genebody, utrs not. This is more work and a bit cumbersome without bioinformatics expertise. If needed, the CSF BioComp group will certainly assist in this task.

Hope that helps

Kind regards,

answered Jan 16, 2015 by Markus.Jaritz (540 points)
0 votes
They will hate me for this :-) but here's a tip: contact the Knowledge Hub users "trupke" and/or "Markus.Jaritz" via sending them an internal message (go to the Users tab, and then look for these usernames).

These users have considerable expertise in motif searches. Would be nice if they could share it through the Knowledge Hub :-)

Cheers, AndrĂ¡s
answered Dec 16, 2014 by aszodi (590 points)