scilogo: a letter to Science about sequence logos not being properly cited

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:

@article{Schneider.Stephens1990,
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"}

• BiBTeX reference:

  The paper was submitted to Science but they never responded!
  

• Here is an omission of any reference (has a protein logo): Caldovic et al. Human Mutation 25(3):293-299, 2005. They are also missing error bars.
• Here is an error (Berkeley weblogo link but no citations): Bioinformatics. 2005 Feb 22 A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. Favorov AV, Gelfand MS, Gerasimova AV, Ravcheev DA, Mironov AA, Makeev VJ.

• 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.

  Dr. Wang kindly provided the raw sequences from which the BZR1 aligned listing and logo (pdf) was created using standard Delila tools.

• BMC Genomics. 2003 Jan 16;4(1):1, Comparative study of methyl-CpG-binding domain proteins. Roloff TC, Ropers HH, Nuber UA.

If you need background information about information theory you can explore my web site. You may find these two resources particularly useful:

• Information Theory Primer, With an Appendix on Logarithms
• A Glossary for Molecular Information Theory and the Delila System.
  A good starting point would be the definition of a bit.

Schneider Lab
origin: 2005 Mar 28
updated: 2006 Feb 25