Hi, I am writing a script to search for motifs in DNA sequence. A user of this program would input at the command line, their fasta file containing the DNA sequence string, and a particular motif to search for. I wish to use the substr() function to search for the particular motif. So far, this is easy enough to do when using A = A, T = T, C = C, and G = G. However, I would like to add the rest of the IUPAC code so that users may define motifs such as ATCNRC, where N = A, T, C, or G and R = A or G? The full IUPAC nucleic acid code is below. 


A = '[A]';
C = '[C]';
G = '[G]';
T = '[T]';
R = '[AG]';
Y = '[CT]';
M = '[AC]';
K = '[GT]';
W = '[AT]';
S = '[GC]';
B = '[CGT]';
D = '[AGT]';
H = '[ACT]';
V = '[ACG]';
N = '[ACGT]';

[download]
Thanks for any help!

In reply to Defining substring matches by drhicks

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