Summary: When sequence logos are used in a paper, it is appropriate to cite the original paper. If the WebLogo server is used, both papers should be cited, as given on the WebLogo page.
The appropriate citation is:
author = "T. D. Schneider
and R. M. Stephens",
title = "Sequence Logos: A New Way to Display Consensus Sequences",
journal = "Nucleic Acids Res.",
volume = "18",
pages = "6097-6100",
year = "1990"}
The paper was submitted to Science but they never responded!
2005 April 1: In this case the display is not a sequence logo, but is called one and there is no reference:
Science. 2005 Mar 11;307(5715):1634-8. BZR1 is a transcriptional repressor with dual roles in brassinosteroid homeostasis and growth responses. He JX, Gendron JM, Sun Y, Gampala SS, Gendron N, Sun CQ, Wang ZY.The figure is incorrect because the scale given is in bits, 0 to 2, yet some positions clearly have variation and so are definitely NOT two bits. The figure was generated by the WebLogo Server with the "Uniform Height" box checked. This will not result in a sequence logo but rather in a frequency diagram. The WebLogo server will be corrected to fix the display. The figure is also missing the small sample correction and error bars which should generally be provided for readers.
If you need background information about information theory you can explore my web site. You may find these two resources particularly useful:
origin: 2005 Mar 28
updated: 2006 Feb 25