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A sequence logo is a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. The width of the stack is proportional to the fraction of valid symbols in that position. (Positions with many gaps have thin stacks.) In general, a sequence logo provides a richer and more precise description of, for example,a binding site, than would a consensus sequence. | A sequence logo is a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. The width of the stack is proportional to the fraction of valid symbols in that position. (Positions with many gaps have thin stacks.) In general, a sequence logo provides a richer and more precise description of, for example,a binding site, than would a consensus sequence. | ||
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==Available versions== | ==Available versions== | ||
Revision as of 02:00, 10 August 2012
Description
WebLogo is an application designed to make the generation of sequence logos as easy and painless as possible.
A sequence logo is a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. The width of the stack is proportional to the fraction of valid symbols in that position. (Positions with many gaps have thin stacks.) In general, a sequence logo provides a richer and more precise description of, for example,a binding site, than would a consensus sequence.
Available versions
- 3.1 (EL5, Galaxy)
- 3.3 (EL6)
Running the application using modules
To use weblogo with the environment modules system at HPC the following commands are available:
Get module information for weblogo:
$module spider weblogo
Load the default application module:
$module load weblogo
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_WEBLOGO_DIR - directory where weblogo is located.
Citation
If you publish research that uses weblogo you have to cite it as follows: Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator, Genome Research, 14:1188-1190, (2004)
Schneider TD, Stephens RM. 1990. Sequence Logos: A New Way to Display Consensus Sequences. Nucleic Acids Res. 18:6097-6100