Author: Dr. Chengpeng Bi,
Copyright (C) 2003-2013 Children's Mercy Hospitals, Kansas City, Missouri USA
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Bi-Logo Plotter can draw either bipartite or traditional single-block sequence logos.
A pair of frequency matrices derived from a set of aligned sequences is required for a bipartite logo.
Each matrix contains a header line followed by 4 tab delimited columns respectively corresponding to
the number of sites containing dA, dC, dG, and dT at a particular position in the alignment.
For a bipartite logo, the first matrix is defined using a header beginning with ">M1" and the second matrix
with ">M2". Single-block logos require only the first matrix. Each element in the matrix must contain a
positive integer, and each row will be converted to frequencies by normalizing the total number of sequences
to 100% or probability of 1.0. There are four transforming operations on the original matrice: (1) none;
(2) first; (3) second; or (4) both. "none" option plots based on the original matrice; "first" means
tranforming the first matrix by complementing and then reversing it.
Here is the transformed output from the working example.
Last modified: April 18, 2011 by Charlie Bi, Children's Mercy Hospitals, Kansas City, Missouri USA