Recommended Tools For De Novo Motif Discovery In Vertebrate Genome Tsses?
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10.2 years ago

What would be the recommended tools I should try for de novo motif discovery in TSS regions (~1-2KB window around the TSS) of non-model vertebrate genomes?

I've been told I should try CisFinder (http://lgsun.grc.nia.nih.gov/CisFinder), but would like to know of other options for comparison.

motif • 2.1k views
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10.2 years ago
Ryan Dale 5.0k

There's been a lot of work recently on MEME to support ChIP-seq-scale data -- see the MEME-ChIP paper and the MEME-ChIP submission form to jump right in.

As part of the standard pipeline, MEME-ChIP also runs DREME, which finds shorter motifs that standard MEME has a hard time with.

I've found MEME-ChIP very easy to use with nice HTML output, and the results I get are consistent with previous work.

It's probably still best to run another algorithm that uses a different strategy -- see this article in Nature Biotechnology for a great intro on the various strategies like enumeration, deterministic optimization, and probabilistic optimization.

Weeder (paper) might be a good choice for this; it was developed specifically for TSSs. However I'm not sure how well it handles big data so you might need to send it random subsamples of your data.

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It has been over a year since I looked at MEME for ChIP-seq data. I will have another look at it thanks.

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10.2 years ago

What type of data do you have?

I do not have any experience with CisFinder. The MEME suite (ref) is commonly used but it can break with 'big data' (sorry I have no quantification on this). We have also had some success with Gimmemotifs for chip-seq data.

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I would suggest the MEME suite too.

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10.2 years ago
Farhat ★ 2.9k

There are a large number of programs that find motifs with different methodologies. This paper compares a number of different programs. The paper is a bit old but most of the algorithms described in it have been updated with the times.

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