HMMEditor stands for profile Hidden Markov Model (pHMM) Visual Editor. It is a tools to visualize and edit pHMM in HMMer format. HMMer format is also used by Pfam protein database. Unique features of HMMEditor includes:
We host a java web start application at http://bioserver.cs.ucf.edu/hmmeditor/. You can launch the application using any web browser supporting java. The minimum required JRE version is 1.5. Alternatively, you can download a source code release at http://bioserver.cs.ucf.edu/hmmeditor/downloads.html, build the software and launch it on your own computer. We have tested HMMEditor on numerous operating systems including Windows and Linux.
With HMMEditor, you can:
Hmm Logo is a way to visualize pHMM in a histogram graph. In HMMEditor, it is one of several views to visualize a pHMM. If generating Hmm Logo is your primary goal, please goto Hmm Logo website, they generate better Logo than HMMEditor.
We have following limitation in HMMEditor 1.0:
Use HMMEditor bug report form. We will try our best to fix a bug; however, there is no garentee for us to fix a specific bug.
Since HMMEditor 1.1, we support Pfam directly from HMMEditor. You can download Pfam database as a large text file here, unzip it, and you will be able to access individual pHmm inside Pfam database directly from HMMEditor.