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MEME 4.6: MEME-ChIP and Spamo

by A. Bretaudeau on February 3, 2011

As promised in one of my last post, I’ve just finished updating our MEME server to the fresh version 4.6.0.

The main new features of this release is the addition of two new applications in the suite: MEME-ChIP and Spamo.


MEME-ChIP logoAs you may guess, MEME-ChIP is dedicated to… ChIP-Seq experiments!

This tool is in fact a meta-tool that launch several analysis on a set of sequences. The good news is that the official website has a great tutorial explaining how it works.

Briefly, the input data is a fasta file containing many sequences generated by ChIP-seq (or other technology producing the same kind of sequences). The first step is to find motifs in these sequences: two tools are launched in parallel: MEME and DREME. MEME is good for finding wider motifs than DREME. DREME is designed for shorter one.

Once it has found a lot of motifs (hopefully), the next step is to compare them to public databanks of motifs, like Jaspar for example. This is done using TOMTOM.

MEME-ChIP then launches a MAST search to find each motif site in the sequences you submitted. Finally AMA and AME are used to estimate the binding affinity of input sequences to each motif, and to find subtly enriched known binding motifs in your input sequences.

So a new tool specialized in ChIP-seq data analysis.


Spamo logo
Spamo is also a tool particularly useful for ChIP-seq (though it can work with other data).

You give it a set of sequences (typically ChIP-seq sequences) and a motif that is represented in some of these sequences. The third thing to specify is a databank of motifs like Jaspar or Uniprobe.

Spamo searches for all motifs of the given databank near the motif sites in your sequences.

So this tool can help you determine the presence of a known motif at a specific position near another one. Useful when studying transcription factor binding sites.

It seems Spamo is still in a beta version, but I didn’t have any bug with it.

That’s it with the 4.6 MEME release!

From → Tools

  1. Prashant Srivastava permalink

    I am currently using Spamo for analysing ~9,000 short sequences (100-200 bp) with transfac matrices … if I try to run the program under high stingency condition i.e. p value < 10e-6 program works but as soon as I go with the default parameters it gives segmentation error. Can you please comment/suggest on this

  2. Hi,
    This could be a bug in spamo. I think the best is to contact the authors of meme and see if they can find a solution. Their address is

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