WebLogo: a sequence logo generator

Genome Res. 2004 Jun;14(6):1188-90. doi: 10.1101/gr.849004.


WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Each logo consists of stacks of letters, one stack for each position in the sequence. The overall height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of symbols within the stack reflects the relative frequency of the corresponding amino or nucleic acid at that position. WebLogo has been enhanced recently with additional features and options, to provide a convenient and highly configurable sequence logo generator. A command line interface and the complete, open WebLogo source code are available for local installation and customization.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence*
  • Base Sequence*
  • Computer Graphics*
  • Cyclic AMP Receptor Protein / chemistry
  • DNA, Bacterial / chemistry
  • Escherichia coli Proteins / chemistry
  • Internet*
  • Nucleic Acid Conformation
  • Protein Structure, Quaternary
  • Software*


  • Cyclic AMP Receptor Protein
  • DNA, Bacterial
  • Escherichia coli Proteins