Home > FR3DSource > xFlankingPairs.m

xFlankingPairs

PURPOSE ^

xFlankingPairs identifies nucleotides on the same strand which make

SYNOPSIS ^

function [File] = xFlankingPairs(File)

DESCRIPTION ^

 xFlankingPairs identifies nucleotides on the same strand which make

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 % xFlankingPairs identifies nucleotides on the same strand which make
0002 function [File] = xFlankingPairs(File)
0003 
0004 E = triu(fix(abs(File.Edge))==1) .* (File.Range == 0); % nested cWW's, i < j
0005 X = (File.Range == 0) .* (abs(File.Edge) > 0) .* (abs(File.Edge) < 15);
0006 
0007 H = sparse(zeros(File.NumNT,File.NumNT));              % to indicate flanks
0008 
0009 [i,j] = find(E);                      % indices of NT's making nested cWW's
0010 
0011 a = [i; j];                           % all indices of nested cWW pairs
0012 
0013 a = sort(a);                          % put them into one list
0014 
0015 for k = 1:(length(a)-1),              % run through all NT making nested cWW
0016   if a(k+1) - a(k) > 1,               % where there is a gap in the number,
0017     H(a(k),a(k+1)) = 1;               % these two flank something
0018   end
0019 end
0020 
0021 H = H + H';                           % symmetrize H
0022 
0023 File.Flank = H;                       % store
0024

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