Sequence logo

A sequence logo in bioinformatics is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences).cite journal |author=Schneider TD, Stephens RM |title=Sequence Logos: A New Way to Display Consensus Sequences |url=http://www.lecb.ncifcrf.gov/~toms/paper/logopaper/ |journal=Nucleic Acids Res |volume=18 |issue=20 |pages=6097–6100 |year=1990 |pmid=2172928 |doi=10.1093/nar/18.20.6097]

To create sequence logos, related DNA, RNA or protein sequences, or DNA sequences that have common conserved binding sites, are aligned so that the most conserved parts create good alignments. A sequence logo can then be created from the conserved multiple sequence alignment. The sequence logo will show how well residues are conserved at each position: the fewer the number of residues, the higher the letters will be, because the better the conservation is at that position. Different residues at the same position will be scaled according to their frequency. Sequence logos can be used to represent conserved DNA binding sites, where transcription factors bind.

References

External links

* [http://www.lecb.ncifcrf.gov/~toms/how.to.read.sequence.logos/ How to read sequence logos] .
* [http://www.genome.org/cgi/content/abstract/14/6/1188 WebLogo: A Sequence Logo Generator] (Publication with full-text access).
* [http://moraine.cebitec.uni-bielefeld.de/files/moraine_ib08.pdf MoRAine] (A web server for sequence logo generation and computational transcription factor binding motif re-annotation - Publication with full-text access).

Tools for creating sequence logos

* [http://code.google.com/p/weblogo/ WebLogo Python Code] Python Code (BSD license, somewhat difficult to use)
* [http://weblogo.berkeley.edu WebLogo] (Online)
* [http://moraine.cebitec.uni-bielefeld.de MoRAine] (Online application with integrated binding site re-annotation)
* [http://biogenio.com/logo/ GENIO] (Online)
* [http://www.bionut.ki.se/groups/tbu/logobar/ LogoBar] (Java application)