Sequence logos: a new way to display consensus sequences

Published on Jan 1, 1990in Nucleic Acids Research 11.56
· DOI :10.1093/nar/18.20.6097
Thomas D. Schneider38
Estimated H-index: 38
,
R M Stephens1
Estimated H-index: 1
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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  • Citations (2240)
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References2
Published on Jan 1, 1985
Kathleen Jensen1
Estimated H-index: 1
,
Niklaus Wirth32
Estimated H-index: 32
+ 6 AuthorsJuris Hartmanis38
Estimated H-index: 38
This manual is directed to those who have previously acquired some programming skill. The intention is to provide a means of learning Pascal without outside guidance. It is based on The Programming Language Pascal (Revised Report) [1]--the basic definition of Pascal and concise reference manual for the experienced Pascal programmer. The linear structure of a book is by no means ideal for introducing a language, whether it be a formal or natural one. Nevertheless, it is recommended to follow the ...
616 Citations
Published on Jan 1, 1983
Edward R. Tufte11
Estimated H-index: 11
(Princeton University)
Slik lyder tre av omtalene av Edward Tuftes The visual display of quantitative information. Siden forste utgave kom ut i 1983, har den blitt sett pa som en tidlos klassiker og bestselger innen informasjonsgrafikk. Siden har den hatt tre «oppfolgere»: Envisioning information (1990), Visual explanations (1997) og Beautiful Evidence (2006). Med sin hoye kompetanse innen informasjonsgrafikk blir Edward Tufte i dag sett pa som en av de fremste pioneerene innen faget, og han har blitt tildelt over 40 ...
5,003 Citations
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Published on Nov 1, 2004in Genomics, Proteomics & Bioinformatics
The NetAcet method has been developed to make predictions of N-terminal acetylation sites, but more information of the data set could be utilized to improve the performance of the model. By employing a new way to extract patterns from sequences and using a sample balancing mechanism, we obtained a correlation coefficient of 0.85, and a sensitivity of 93% on an independent mammalian data set. A web server utilizing this method has been constructed and is available at http://166.111.24.5/acetylati...
12 Citations Source Cite
Published on Dec 31, 2001in Methods in Enzymology 1.98
Thomas A. Hall4
Estimated H-index: 4
,
James W. Brown31
Estimated H-index: 31
33 Citations Source Cite
Published on Jan 1, 2015in Methods of Molecular Biology
Tobias Ehrenberger7
Estimated H-index: 7
(Massachusetts Institute of Technology),
Lewis C. Cantley162
Estimated H-index: 162
(Harvard University),
Michael B. Yaffe89
Estimated H-index: 89
(Massachusetts Institute of Technology)
The prediction of protein-protein interactions and kinase-specific phosphorylation sites on individual proteins is critical for correctly placing proteins within signaling pathways and networks. The importance of this type of annotation continues to increase with the continued explosion of genomic and proteomic data, particularly with emerging data categorizing posttranslational modifications on a large scale. A variety of computational tools are available for this purpose. In this chapter, we r...
34 Citations Source Cite
Published on Jan 1, 2012in Science & Engineering Faculty
Exponential growth of genomic data in the last two decades has made manual analyses impractical for all but trial studies. As genomic analyses have become more sophisticated, and move toward comparisons across large datasets, computational approaches have become essential. One of the most important biological questions is to understand the mechanisms underlying gene regulation. Genetic regulation is commonly investigated and modelled through the use of transcriptional regulatory network (TRN) st...
Published on Mar 1, 2003in Molecular Genetics and Genomics 2.73
N. Guimond1
Estimated H-index: 1
(University of Maryland Biotechnology Institute),
Dennis K. Bideshi22
Estimated H-index: 22
(University of California)
+ 2 AuthorsDavid A. O'Brochta26
Estimated H-index: 26
(University of Maryland Biotechnology Institute)
Transposable elements are being developed as tools for genomics and for the manipulation of insect genotypes for the purposes of biological control. An understanding of their transposition behavior will facilitate the use of these elements. The behavior of an autonomous Hermes transposable element from Musca domestica in the soma and germ-line of Drosophila melanogaster was investigated using the method of transposon display. In the germ-line, Hermes transposed at a rate of approximately 0.03 ju...
48 Citations Source Cite
Published on Jan 1, 2013in Methods of Molecular Biology
Lihua Julie Zhu31
Estimated H-index: 31
(University of Massachusetts Medical School)
20 Citations Source Cite
Published on Jan 1, 2008in Methods of Molecular Biology
Timothy L. Bailey52
Estimated H-index: 52
(University of Queensland)
Sequence motif discovery algorithms are an important part of the computational biologists toolkit. The purpose of motif discovery is to discover patterns in biopolymer (nucleotide or protein) sequences in order to better understand the structure and function of the molecules the sequences represent.
34 Citations Source Cite
Published on Jan 1, 2001in Current Topics in Membranes 3.51
Henning Stahlberg44
Estimated H-index: 44
(University of Basel),
Bernard Heymann (University of Basel)+ 2 AuthorsAndreas Engel95
Estimated H-index: 95
(University of Basel)
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Published on Jan 1, 2007
Jan Grau14
Estimated H-index: 14
,
Jens Keilwagen14
Estimated H-index: 14
(Leibniz Association)
+ 2 AuthorsStefan Posch13
Estimated H-index: 13
Markov models have been proposed for the classification of DNA-motifs using generative approaches for parameter learning. Here, we propose to apply the discriminative paradigm for this problem and study two different priors to facilitate parameter estimation using the maximum supervised posterior. Considering seven sets of eukaryotic transcription factor binding sites we find this approach to be superior employing area under the ROC curve and false positive rate as performance criterion, and bet...
4 Citations