Weblogo
is a web-based server to create Sequence Logos,
written by Steve Brenner's group.
Sequence logos
are a graphical technique for displaying a summary of
a set of aligned sequences invented in the Schneider lab.
The original paper is available.
Although weblogo is highly useful for biologists to generate
logos, like any other tool it can be misused.
Below are recommendations for proper use of the logos so that
they provde useful data for further studies.
Links to the
Glossary are provided.
The notation
link needed
means that I need to add a link
to another point in this website to explain the point in more detail.
- Chose a sensible
coordinate system. The
zero coordinate
is used
in
sequence walkers, so it is important to have a zero somewhere in the
sequence. Usually we chose a well conserved base.
link needed
- Keep the word 'bits' on the logo. Bits are a unit of measure.
link needed
- Bits are not scores.
link needed
- Report the total information content of the logo. This is an
important number called Rsequence. It is generally related to the
size of the genome and number of sites. See the paper on Ev and run
the Evj program to see how this works.
link needed
- If your binding site is symmetric, publish a symmetrical
sequence logo.
link needed
- Publish error bars. Without these one cannot tell how good the
logo is.
- Publish the number of sequences used to create the logo,
preferably on the logo image itself.
- For DNA (and even RNA!) put a sine wave on the logo and align it
with major and minor grooves. This makes interesting predictions!
link needed
- Sequence logos are NOT consensus sequences!
See this paper:
Consensus Sequence Zen.
- Cite the
original reference:
@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",
pmid = "2172928",
pmcid = "PMC332411",
year = "1990"}
so that your paper can be tracked
in the literature.
