@article{Schneider1986,
title = "Information content of binding sites on nucleotide sequences",
journal = "Journal of Molecular Biology",
volume = "188",
number = "3",
pages = "415 - 431",
year = "1986",
issn = "0022-2836",
doi = "https://doi.org/10.1016/0022-2836(86)90165-8",
url = "http://www.sciencedirect.com/science/article/pii/0022283686901658",
author = "Thomas D. Schneider and Gary D. Stormo and Larry Gold and Andrzej Ehrenfeucht",
abstract = "Repressors, polymerases, ribosomes and other macromolecules bind to specific nucleic acid sequences. They can find a binding site only if the sequence has a recognizable pattern. We define a measure of the information (Rsequence) in the sequence patterns at binding sites. It allows one to investigate how information is distributed across the sites and to compare one site to another. One can also calculate the amount of information (Rfrequency) that would be required to locate the sites, given that they occur with some frequency in the genome. Several Escherichia coli binding sites were analyzed using these two independent empirical measurements. The two amounts of information are similar for most of the sites we analyzed. In contrast, bacteriophage T7 RNA polymerase binding sites contain about twice as much information as is necessary for recognition by the T7 polymerase, suggesting that a second protein may bind at T7 promoters. The extra information can be accounted for by a strong symmetry element found at the T7 promoters. This element may be an operator. If this model is correct, these promoters and operators do not share much information. The comparisons between Rsequence and Rfrequency suggest that the information at binding sites is just sufficient for the sites to be distinguished from the rest of the genome."
}

@article{Schneider1990,
    author = {Schneider, Thomas D. and Stephens, R.Michael},
    title = "{Sequence logos: a new way to display consensus sequences}",
    journal = {Nucleic Acids Research},
    volume = {18},
    number = {20},
    pages = {6097-6100},
    year = {1990},
    month = {10},
    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.}",
    issn = {0305-1048},
    doi = {10.1093/nar/18.20.6097},
    url = {https://doi.org/10.1093/nar/18.20.6097},
    eprint = {https://academic.oup.com/nar/article-pdf/18/20/6097/3939026/18-20-6097.pdf},
}

@book{Chambers1998,
    author = {Chambers, John M.},
    title = {Programming with data: A guide to the S language},
    publisher = {Springer},
    place = {New York},
    year = {1998},
    ISBN = {978-0-387-98503-9}
}
