CodonLogo 1.0

· about · create · examples · manual ·
   
CodonLogo

Introduction

Codonlogo is based on WebLogo,a web based application designed to make the generation of sequence logos easy and painless.CodonLogo Extends Weblogo to allow generation of sequence logos with codons rather than amino acids or nucleotides.

Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens. 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 codon at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.

References

Crooks GE, Hon G, Chandonia JM, Brenner SE CodonLogo: A sequence logo generator,
Genome Research, 14:1188-1190, (2004) [Full Text ]

Schneider TD, Stephens RM. 1990. Sequence Logos: A New Way to Display Consensus Sequences. Nucleic Acids Res. 18:6097-6100

Disclaimer

While no permanent records are kept of submitted sequences, we cannot undertake to guarantee that data sent to CodonLogo remains secure. Moreover, no guarantees whatsoever are provided about data generated by CodonLogo.

Feedback

Suggestions on how to improve CodonLogo are heartily welcomed! Please direct questions to murphy.david@gmail.com

a