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. 1990 Oct 25;18(20):6097–6100. doi: 10.1093/nar/18.20.6097

Sequence logos: a new way to display consensus sequences.

T D Schneider 1, R M Stephens 1
PMCID: PMC332411  PMID: 2172928

Abstract

A graphical method is presented for displaying the patterns in a set of aligned sequences. The characters representing the sequence are stacked on top of each other for each position in the aligned sequences. The height of each letter is made proportional to its frequency, and the letters are sorted so the most common one is on top. The height of the entire stack is then adjusted to signify the information content of the sequences at that position. From these 'sequence logos', one can determine not only the consensus sequence but also the relative frequency of bases and the information content (measured in bits) at every position in a site or sequence. The logo displays both significant residues and subtle sequence patterns.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bashford D., Chothia C., Lesk A. M. Determinants of a protein fold. Unique features of the globin amino acid sequences. J Mol Biol. 1987 Jul 5;196(1):199–216. doi: 10.1016/0022-2836(87)90521-3. [DOI] [PubMed] [Google Scholar]
  2. Fields C. Information content of Caenorhabditis elegans splice site sequences varies with intron length. Nucleic Acids Res. 1990 Mar 25;18(6):1509–1512. doi: 10.1093/nar/18.6.1509. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Gold L., Pribnow D., Schneider T., Shinedling S., Singer B. S., Stormo G. Translational initiation in prokaryotes. Annu Rev Microbiol. 1981;35:365–403. doi: 10.1146/annurev.mi.35.100181.002053. [DOI] [PubMed] [Google Scholar]
  4. Hein J. Unified approach to alignment and phylogenies. Methods Enzymol. 1990;183:626–645. doi: 10.1016/0076-6879(90)83041-7. [DOI] [PubMed] [Google Scholar]
  5. Sadler J. R., Waterman M. S., Smith T. F. Regulatory pattern identification in nucleic acid sequences. Nucleic Acids Res. 1983 Apr 11;11(7):2221–2231. doi: 10.1093/nar/11.7.2221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Schneider T. D., Stormo G. D. Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique. Nucleic Acids Res. 1989 Jan 25;17(2):659–674. doi: 10.1093/nar/17.2.659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Schneider T. D., Stormo G. D., Gold L., Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J Mol Biol. 1986 Apr 5;188(3):415–431. doi: 10.1016/0022-2836(86)90165-8. [DOI] [PubMed] [Google Scholar]
  8. Schneider T. D., Stormo G. D., Haemer J. S., Gold L. A design for computer nucleic-acid-sequence storage, retrieval, and manipulation. Nucleic Acids Res. 1982 May 11;10(9):3013–3024. doi: 10.1093/nar/10.9.3013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Schneider T. D., Stormo G. D., Yarus M. A., Gold L. Delila system tools. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):129–140. doi: 10.1093/nar/12.1part1.129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Shine J., Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. doi: 10.1073/pnas.71.4.1342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Stormo G. D. Consensus patterns in DNA. Methods Enzymol. 1990;183:211–221. doi: 10.1016/0076-6879(90)83015-2. [DOI] [PubMed] [Google Scholar]

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