sequence logos (序列logo图)

Sequence logos for MATLAB

Basic usage

S = {'ATTATAGCAAACTA';
     'AACATGCCAAAGTA';
     'ATCATGCAAAAGGA'};
% S = ['ATTATAGCAAACTA';
%      'AACATGCCAAAGTA';
%      'ATCATGCAAAAGGA'];
figure()
% Default: 'Bits' method, 'NT' type, small-sample correction enabled('SSC','on').
seqLogo(S)

figure()
% Disable small-sample correction.
seqLogo(S, 'SSC','off')

figure()
% 'Prob'(Probability) method
seqLogo(S, 'Method', 'Prob')

figure()
% 'Prob' (Probability) method, 
% with sequence positions restricted to the range of 2 to 6
seqLogo(S, 'Method', 'Prob', 'Range',[2,6])

Amino acid type

S = readcell("seqlogo_protein_3.txt");

figure()
% 'Bits' method, 'AA' type, disable small-sample correction
seqLogo(S, 'Type','AA', 'SSC','off')

figure()
% 'Prob' method, 'AA' type, disable small-sample correction
seqLogo(S, 'Type','AA', 'SSC','off', 'Method','Prob')

Change color for nucleotide type

S = readcell("seqlogo_DNA.txt");

Color = {'C',[205,255,101]./255, 'A',[104,101,255]./255, 'TU',[164,230,101]./255, 'G',[104,203,254]./255};
% Color = {'C',[127,91,93]./255, 'A',[187,128,110]./255, 'TU',[197,173,143]./255, 'G',[59,71,111]./255};

figure()
seqLogo(S, 'Color',Color)

figure()
seqLogo(S, 'Method','Prob', 'Color',Color) 

Change color for amino acid type

S = readcell("seqlogo_protein_3.txt");

Color = {'CDEFH',[205,255,101]./255, 'AIKLM',[104,101,255]./255, 'TUNPQR',[164,230,101]./255, 'GSVWY',[104,203,254]./255};
% Color = {'CDEFH',[127,91,93]./255, 'AIKLM',[187,128,110]./255, 'TUNPQR',[197,173,143]./255, 'GSVWY',[59,71,111]./255};

figure()
seqLogo(S, 'Color',Color, 'Type','AA')

figure()
seqLogo(S, 'Method','Prob', 'Color',Color, 'Type','AA')