Almeida, J.S., S.Vinga (2006) Computing distribution of scale independent motifs in biological sequences. Algorithms for Molecular Biology. 1:18. [PMID:17049089].
link for USM tbox
The main function of this MATLAB library is usm.m, which has detailed help documentation including examples of usage.
Another way to learn about the toolbox and particularly the use of its graphic display capabilities is to generate the four figures in the manuscript by using paper_fig(#), where "#" stands for the figure number (there are 4).
e.g. to generate figure 1: