A web-based program (WHAT) for the simultaneous prediction of hydropathy, amphipathicity, secondary structure and transmembrane topology for a single protein sequence.

We designed a web-based program, WHAT, which uses a sliding window to determine and plot the hydropathy, amphipathicity, secondary structure and transmembrane topology along the length of any protein sequence. This method is based on programs designed by us for hydropathy and amphipathicity but on JNET and MEMSAT for secondary structure and transmembrane topology predictions, respectively. It has a user-friendly interface and a convenient input format. It is available at our website http://www.biology.ucsd.edu/~yzhai/biotools.html.