Movies of Logos Generated from a Natural Frequency Table

Jiggling sequence logo movie created from 50 generated
sequence logos each built from 100 randomly made donor site

The frequency table for 1799 donor sites (Stephens and Schneider J. Mol. Biol., 228, 1124-1136, 1992), f(b,l) (where b is the base A,C,G or T and l is the position in the site) was used with a random number generator to create 100 sequences that resemble donor sites. These sequences were used used to create a sequence logo. Since there were only 100 sequences, the resulting logo is slightly different from the original.

The process described above was repeated 50 times and the logos were combined using the imagemagick convert program to make the movie.

The logo jiggles because 100 is a small (!) number of samples. This method gives one a sense for how much a logo varies depending on sequence.

The program that creates a single distribution from a ribl is ridi.

color bar Small icon for Theory of Molecular Machines: physics,
chemistry, biology, molecular biology, evolutionary theory,
genetic engineering, sequence logos, information theory,
electrical engineering, thermodynamics, statistical
mechanics, hypersphere packing, gumball machines, Maxwell's
Daemon, limits of computers

Schneider Lab

origin: 2002 November 1
updated: 2002 November 1
color bar