HMM logo

The HMM logo is a graphical representation of the Hidden Markov Model that decribes the properties of that HMM. The full data on interpreting HMM logos is given here. Put simply, the differing heights and colors of the letters represent different properties of the positions in the HMM they represent.

Fig. 1. An example of the HMM logo from methyl-accepting chemotaxis protein in Halorhabdus utahensis. Only the first few sections of the logo are displayed here; the full logo is too large to display here.

Clicking the name of the Pfam, followed by the "HMM Logo" button on the sidebar, will bring up the HMM Logo.