It is possible to have more than non-standard nucleotide in your sequence? If so, you might consider looking for all the non-matches: 
#!/usr/bin/perl

use warnings;
use strict;

my $dna_input = shift;

my @dna = split( '', $dna_input );
my (@index) = grep { $dna[$_] !~ /[ATCG]/ } 0..$#dna;
print "Non-nucleotide at position $_\n" for @index;

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In reply to Re: If/else within a foreach loop to check strings within an array by drmrgd
in thread If/else within a foreach loop to check strings within an array by Anonymous Monk

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