Bi-Logo Plotter

Author: Dr. Chengpeng Bi, Copyright (C) 2003-2013 Children's Mercy Hospitals, Kansas City, Missouri USA
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Bipartite Sequence Logo Plotter
* logo name:
x-axis label: start:
graph size: X (max: 50cm x 20cm)
* model (freq. matrix: cols 1-4 represnt freqs of A,C,G,T)
central gap: *transform:
*required, *complement and then reverse the specified matrix.

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