Editing Consensus sequence (section)

===Notation===
The conserved sequence motifs are called '''consensus sequences''' and they show which residues are conserved and which residues are variable. Consider the following example [[DNA]] sequence:

:A[CT]N{A}YR

In this [[Sequence motif#Pattern description notations|notation]], A means that an A is always found in that position; [CT] stands for either C or T; N stands for any base; and {A} means any base except A. Y represents any [[pyrimidine]], and R indicates any [[purine]].
In this example, the notation [CT] does not give any indication of the relative frequency of C or T occurring at that position. And it is not possible to write it as a single consensus sequence e.g. ACNCCA.  An alternative method of representing a consensus sequence uses a [[sequence logo]]. This is a graphical representation of the consensus sequence, in which the size of a symbol is related to the frequency that a given nucleotide (or amino acid) occurs at a certain position. In sequence logos the more conserved the residue, the larger the symbol for that residue is drawn; the less frequent, the smaller the symbol. Sequence logos can be generated using [http://weblogo.berkeley.edu/ WebLogo], or using the [http://db.systemsbiology.net/gestalt/ Gestalt Workbench], a publicly available visualization tool written by Gustavo Glusman at the [http://www.systemsbiology.org Institute for Systems Biology].<ref name="Schneider2002">{{cite journal |author=Schneider TD |title=Consensus Sequence Zen|journal=Appl Bioinform |volume=1 |issue=3 |pages=111–119 |year=2002 |pmid=15130839 |pmc=1852464}}</ref>