WebLogo: a sequence logo generator.

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 year

  2004

• Venue

  Genome Research

• Publication date

  2004-06-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1101/GR.849004PMID 15173120PMCID PMC419797
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The Pfam protein families database

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• Elements of Information Theory

  2005cited by this paper
• WebLogo: a sequence logo generator.

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• An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands.

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• Information content and free energy in DNA--protein interactions.

  1998influential reference
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  1998influential reference
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  1991influential reference
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  1990influential reference
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  1989cited by this paper
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  1988cited by this paper
• Information content of binding sites on nucleotide sequences.

  1986influential reference
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