Sequence logos: a powerful, yet simple, tool

A powerful technique for analyzing DNA and protein sequences, the sequence logo, is now available to researchers. The authors explain sequence logos, to show their usefulness for biological and linguistic research, and to encourage their use by others. A sequence logo is a graphic representation of the amount of information to be found in a set of DNA, RNA, or protein sequences. This method has advantages over the conventional method of creating a consensus. For example, a logo of DNA shows all the bases found in the binding site of a protein, indicates how much each base is conserved, and depicts the location of the conservation with respect to the major and minor grooves of the DNA.<<ETX>>

[1]  N. Seeman,et al.  Sequence-specific Recognition of Double Helical Nucleic Acids by Proteins (base Pairs/hydrogen Bonding/recognition Fidelity/ion Binding) , 2022 .

[2]  M Ptashne,et al.  Autoregulation and function of a repressor in bacteriophage lambda. , 1976, Science.

[3]  T. D. Schneider,et al.  Information content of binding sites on nucleotide sequences. , 1986, Journal of molecular biology.

[4]  M. Tribus.  Thermostatics and thermodynamics , 1961 .

[5]  C. E. SHANNON,et al.  A mathematical theory of communication , 1948, MOCO.

[6]  T. D. Schneider,et al.  Theory of molecular machines. I. Channel capacity of molecular machines. , 1991, Journal of theoretical biology.

[7]  T. D. Schneider,et al.  Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.

[8]  D B Davison,et al.  The GenBank-Server at the University of Houston. , 1990, Nucleic acids research.

[9]  M Ptashne,et al.  How the lambda repressor and cro work. , 1980, Cell.

[10]  T D Schneider,et al.  High information conservation implies that at least three proteins bind independently to F plasmid incD repeats , 1992, Journal of bacteriology.

[11]  P. Griffiths,et al.  Electronic communications and the new biology. , 1992, Nucleic Acids Research.

[12]  Claude E. Shannon,et al.  The Mathematical Theory of Communication , 1950 .

[13]  Thomas D. Schneider.  Information and Entropy of Patterns in Genetic Switchs , 1988 .

[14]  T. D. Schneider,et al.  Theory of molecular machines. II. Energy dissipation from molecular machines. , 1991, Journal of theoretical biology.

[15]  T D Schneider,et al.  Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique. , 1989, Nucleic acids research.