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@article{Bindewald.Shapiro2006,
author = "E. Bindewald
and T. D. Schneider
and B. A. Shapiro",
title = "{CorreLogo: An online server for 3D sequence logos of RNA and
DNA alignments}",
journal = "Nucleic Acids Res.",
volume = "34",
pages = "w405--w411",
pmid = "16845037",
pmcid = "PMC1538790",
note = "
\url{https://doi.org/10.1093/nar/gkl269},
\url{https://alum.mit.edu/www/toms/papers/correlogo/},
\url{https://rnastructure.cancer.gov/correlogo/}",
year = "2006"}
A 3D sequence logo of tRNAs is displayed using data generated by an on-line web server, correlogo.ncifcrf.gov. The 3D logo depicts correlations between positions of aligned sequences by stacks of colored bars. The height of each bar is proportional to the frequency of the dinucleotide pair written on two faces. The bars are sorted by size and the total height of the stack is the mutual information between the two positions, measured in bits. Arrows point from the 5' towards the 3' end of the tRNA. Large orange and red stacks represent the complementary helical stems of the tRNA. From the left to the right the taller stacks are: the tRNA acceptor stem, the D stem, the anticodon stem, and the TψC stem. Stacks visible to the right of the main diagonal are mirror images of those on the left. In addition, other correlations are visible. A set of low 'buildings' in the center of the square 'city' have orange, yellow and green on the top of their stacks. These correspond to correlations discovered by Mike Yarus between the anticodon 3' nucleotide, known as the cardinal base, and bases of the anticodon stem. In the foreground is a set of low lying stacks with blue, green and yellow tops. These stacks correspond to correlations along the tRNA acceptor stem. Along the left edge are other significant correlations which relate the acceptor stem with the anticodon stem.
@article{Hoffman.Swanstrom2003,
author = "N. G. Hoffman
and C. A. Schiffer
and R. Swanstrom",
title = "{Covariation of amino acid positions in HIV-1 protease}",
journal = "Virology",
volume = "314",
pages = "536--548",
pmid = "14554082",
year = "2003"}
@article{Korber.Lapedes1993,
author = "B. T. Korber
and R. M. Farber
and D. H. Wolpert
and A. S. Lapedes",
title = "{Covariation of mutations in the V3 loop of human
immunodeficiency virus type 1 envelope protein: an information
theoretic analysis}",
journal = "Proc. Natl. Acad. Sci. USA",
volume = "90",
pages = "7176--7180",
pmid = "8346232",
pmcid = "PMC47099",
year = "1993"}
Schneider Lab
origin: 2006 Feb 13
updated: 2024 Apr 18