Hello,

Yes, MEME is not on the Main server, but can be used in local, cloud, or slipstream Galaxy installs. For throughput - there are a few MEME-related repositories in the Tool Shed to choose from. How many sequences each can process will likely vary and are related to the hardware the Galaxy instance is run on. Contacting the tool authors is one path or you can try testing using your actual data. Data composition could be an important factor (not just the number of sequences).

For the Sequence Logo Generator, I do not know of a hard limit by the tool itself, but as the recommended/supported input is ClustalW output, that tool will most likely be setting the potential upper limit when using the public Main Galaxy instance. Testing will be the best way to learn the limits for your particular data (whether nucleotide or protein), but the success range will be capped in the thousands, not millions (and possibly lower, as length increases). If there is a memory problem or the run time exceeds the limits on the public server, the job will end with an error. Moving to a scaled up server, such as a cloud Galaxy, will give you more control over these types of variables.

Some benchmarks are in the Clustal W publication:
http://bioinformatics.oxfordjournals.org/content/23/21/2947.long

If others would like to post benchmarks from their own experience, that would be welcome!

Jen
Galaxy team

On 9/11/13 2:51 PM, Boaz Shaanan wrote:

Hi,

Has the MEME module been taken out of the main galaxy server? Assuming it'll be back, what's roughly a recommended number of sequences to feed into MEME? It has a limit on the sequences that it can digest but I don't know what it is. Likewise, what's this limit for the Sequence Logo Generator?

Thanks,

Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaanan@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710
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