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Some news: hmmer 3 and meme

by A. Bretaudeau on September 22, 2010

Hi all,

September has been a busy month (and it’s not finished…)! But finally, I found some time to work on two things:

Hmmer 3

Copyright © Michael JastremskiHmmer is a suite of tools for the analysis of HMM motifs (remember my post about HMM?).

Hmmer 3 has been officially released on 28 March 2010 and we have installed it on our cluster. If you have an account, you just have to launch the command “source /local/env/envhmmer-3.0”, and you’re ready to use it.

Hmmer is composed of the following programs: hmmalign, hmmbuild, hmmconvert, hmmemit, hmmfetch, hmmscan, hmmsearch, hmmsim, hmmstat, jackhmmer and phmmer.

Now hmmer3 is also available directly from our mobyle server. And I have deployed all the tools of this suite as SOAP webservices on our Opal server too.

I’ll try to show you how to use these tools later, but you can already start to play with it!

You can also have a look at the official documentation which present each tool. It is available here.


MEME is another suite of tools for pattern matching and discovery. For more info, see the official website.

It is composed of a few main tools: MEME, MAST, TOMTOM, GOMO, GLAM2, GLAM2SCAN, FIMO and MCAST. Smaller utilities are available only from command line.

All of them are available from our cluster (source /local/env/envmeme). I have installed the default web interface too and it is available here. And webservices are too available, as usual, from our Opal server.

Like the hmmer suite, I’ll try to describe MEME features later, but you can already try to use it following the documentation available from the web interface.

These tools should also be accessible directly from our mobyle server soon.

That’s all for today…

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