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Literature DB >> 2172928

Sequence logos: a new way to display consensus sequences.

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.

Mesh：

Substances：

Year: 1990 PMID： 2172928 PMCID： PMC332411 DOI： 10.1093/nar/18.20.6097

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

11 in total

1. Consensus patterns in DNA.

Authors: G D Stormo
Journal: Methods Enzymol Date: 1990 Impact factor: 1.600

2. Unified approach to alignment and phylogenies.

Authors: J Hein
Journal: Methods Enzymol Date: 1990 Impact factor: 1.600

3. Determinants of a protein fold. Unique features of the globin amino acid sequences.

Authors: D Bashford; C Chothia; A M Lesk
Journal: J Mol Biol Date: 1987-07-05 Impact factor: 5.469

4. Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique.

Authors: T D Schneider; G D Stormo
Journal: Nucleic Acids Res Date: 1989-01-25 Impact factor: 16.971

Review 5. Translational initiation in prokaryotes.

Authors: L Gold; D Pribnow; T Schneider; S Shinedling; B S Singer; G Stormo
Journal: Annu Rev Microbiol Date: 1981 Impact factor: 15.500

6. Regulatory pattern identification in nucleic acid sequences.

Authors: J R Sadler; M S Waterman; T F Smith
Journal: Nucleic Acids Res Date: 1983-04-11 Impact factor: 16.971

7. Delila system tools.

Authors: T D Schneider; G D Stormo; M A Yarus; L Gold
Journal: Nucleic Acids Res Date: 1984-01-11 Impact factor: 16.971

8. A design for computer nucleic-acid-sequence storage, retrieval, and manipulation.

Authors: T D Schneider; G D Stormo; J S Haemer; L Gold
Journal: Nucleic Acids Res Date: 1982-05-11 Impact factor: 16.971

9. Information content of Caenorhabditis elegans splice site sequences varies with intron length.

Authors: C Fields
Journal: Nucleic Acids Res Date: 1990-03-25 Impact factor: 16.971

10. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites.

Authors: J Shine; L Dalgarno
Journal: Proc Natl Acad Sci U S A Date: 1974-04 Impact factor: 11.205

1429 in total

1. In silico detection of control signals: mRNA 3'-end-processing sequences in diverse species.

Authors: J H Graber; C R Cantor; S C Mohr; T F Smith
Journal: Proc Natl Acad Sci U S A Date: 1999-11-23 Impact factor: 11.205

2. Assessing clusters and motifs from gene expression data.

Authors: L M Jakt; L Cao; K S Cheah; D K Smith
Journal: Genome Res Date: 2001-01 Impact factor: 9.043

3. Effects of saturation mutagenesis of the phage SP6 promoter on transcription activity, presented by activity logos.

Authors: I Shin; J Kim; C R Cantor; C Kang
Journal: Proc Natl Acad Sci U S A Date: 2000-04-11 Impact factor: 11.205

4. Proteomics of the chloroplast: systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins.

Authors: J B Peltier; G Friso; D E Kalume; P Roepstorff; F Nilsson; I Adamska; K J van Wijk
Journal: Plant Cell Date: 2000-03 Impact factor: 11.277

5. cis and trans factors affecting Mos1 mariner evolution and transposition in vitro, and its potential for functional genomics.

Authors: L R Tosi; S M Beverley
Journal: Nucleic Acids Res Date: 2000-02-01 Impact factor: 16.971

9. Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation.

Authors: T D Schneider
Journal: Nucleic Acids Res Date: 2001-12-01 Impact factor: 16.971

10. Structure and evolution of the hAT transposon superfamily.

Authors: E Rubin; G Lithwick; A A Levy
Journal: Genetics Date: 2001-07 Impact factor: 4.562