Hello again ic23oluk,

I spend some time and I got even more confused. I got different results from your scrip:

#!usr/bin/perl
use strict;
use warnings;

my %hash;
my $substring = 'ATG';
my @tags = ('TAG', 'TAA', 'TGA');

while (<>) {
    chomp;
    next if $. < 2; # Skip first line
    my $found = index($_, $substring);
    while ($found != -1) {
    foreach my $tag (@tags) {
        my $position = index($_, $tag, $found + 2);
        $hash{$position} = $tag if ($position != -1);
    }
    my $offset = $found + 1;
    $found = index($_, $substring, $offset);
    }
} continue {
    close ARGV if eof; # reset $.
}

foreach my $position (sort {$a <=> $b} keys %hash) {
    print "Position: $position String: $hash{$position}\n";
}

__END__

$ perl bio.pl sequence.fa
Position: 29 String: TAA
Position: 48 String: TGA
Position: 73 String: TAA
Position: 134 String: TGA
Position: 201 String: TAA
Position: 221 String: TGA
Position: 248 String: TAA
Position: 288 String: TGA
Position: 309 String: TAG
Position: 324 String: TGA
Position: 332 String: TAA
Position: 378 String: TAA
Position: 381 String: TAG
Position: 395 String: TGA
Position: 408 String: TGA
Position: 448 String: TAA
Position: 505 String: TGA
Position: 512 String: TAA
Position: 621 String: TGA
Position: 700 String: TGA
Position: 722 String: TAA
Position: 743 String: TAA
Position: 752 String: TGA
Position: 857 String: TAA
Position: 864 String: TAA
Position: 957 String: TAG
Position: 974 String: TAA
Position: 1002 String: TGA
Position: 1019 String: TAA
Position: 1052 String: TGA
Position: 1198 String: TGA
Position: 1210 String: TAG
Position: 1253 String: TGA
Position: 1265 String: TAA
[download]

At this point I do not know if your script is giving you the correct output. I am not sure if mine also works perfectly but I tried to confirm that by using grep and the tags e.g. TAA to check if I should get an output as my script does and yours skips.

For example:

$ cat sequence.fa | grep TAA
GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+ GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGA
+AA ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGAT
+TCTG TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACT
+GGTTTA GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGA
+TTACTATC TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAA
+TCCGTACGTT TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAAC
+CGAAGATGATTT CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTC
+GCTGCGTTGAGGCT TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTT
+GAGTTTATTGCTGCCG TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCAT
+GGAAGGCGCTGAATTTAC GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGT
+TCGCGTTTACCTTGCGTGTA CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGT
+CAAAAATTACGTGCGGAAGGAG TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGT
+CGTCCGCAGCCGTTGCGAGGTACT AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCA
+ACAATTTTAATTGCAGGGGCTTCGGC CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCG
+CCGAGCGTATGCCGCATGACCTTTCCCA TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACC
+ATTTCAACTACTCCGGTTATCGCTGGCGAC TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTC
+TCCATTGCGTCGTGGCCTTGCTATTGACTCTA CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTC
+ACGTTTATGGTGAACAGTGGATTAAGTTCATGAA

$ cat sequence.fa | grep -o TAA | wc -l
21
[download]

Based on that I can tell that I am getting confident that your script is not calculating something correctly.

Update: I took a look again on the bash search (remember to remove first line from file!):

$ cat sequence.fa | grep -b -o TAA
29:TAA
73:TAA
106:TAA
201:TAA
248:TAA
332:TAA
378:TAA
385:TAA
448:TAA
480:TAA
512:TAA
722:TAA
743:TAA
857:TAA
864:TAA
870:TAA
934:TAA
974:TAA
1008:TAA
1019:TAA
1265:TAA
[download]

The output of my script:

#!usr/bin/perl
use strict;
use warnings;

my $substring = 'TAA';

while (<>) {
    chomp;
    next if $. < 2; # Skip first line
    my $found = index($_, $substring);
    while ($found != -1) { # check for multiple occurrences in the sam
+e string
    print "Found $substring at $found\n";
    my $offset = $found + 1;
    $found = index($_, $substring, $offset);
    }
} continue {
    close ARGV if eof; # reset $.
}

__END__

$ perl bio_2.pl sequence.fa
Found TAA at 29
Found TAA at 73
Found TAA at 106
Found TAA at 201
Found TAA at 248
Found TAA at 332
Found TAA at 378
Found TAA at 385
Found TAA at 448
Found TAA at 480
Found TAA at 512
Found TAA at 722
Found TAA at 743
Found TAA at 857
Found TAA at 864
Found TAA at 870
Found TAA at 934
Found TAA at 974
Found TAA at 1008
Found TAA at 1019
Found TAA at 1265
[download]

Update2: If you check also the ATG

$ perl bio_2.pl sequence.fa
Found ATG at 16
Found ATG at 50
Found ATG at 133
Found ATG at 232
Found ATG at 252
Found ATG at 287
Found ATG at 305
Found ATG at 363
Found ATG at 394
Found ATG at 489
Found ATG at 575
Found ATG at 651
Found ATG at 689
Found ATG at 724
Found ATG at 854
Found ATG at 859
Found ATG at 954
Found ATG at 1014
Found ATG at 1044
Found ATG at 1051
Found ATG at 1145
Found ATG at 1228
Found ATG at 1249
Found ATG at 1272
tinyos@tinyOS:~/Monks$ cat sequence.fa | grep -b -o ATG
16:ATG
50:ATG
133:ATG
232:ATG
252:ATG
287:ATG
305:ATG
363:ATG
394:ATG
489:ATG
575:ATG
651:ATG
689:ATG
724:ATG
854:ATG
859:ATG
954:ATG
1014:ATG
1044:ATG
1051:ATG
1145:ATG
1228:ATG
1249:ATG
1272:ATG
[download]

Now check one by one the index and the final output of my script:

$ perl bio.pl sequence.fa
Position: 29 String: TAA
Position: 48 String: TGA
Position: 73 String: TAA
Position: 134 String: TGA
Position: 201 String: TAA
Position: 221 String: TGA
Position: 248 String: TAA
Position: 288 String: TGA
Position: 309 String: TAG
Position: 324 String: TGA
Position: 332 String: TAA
Position: 378 String: TAA
Position: 381 String: TAG
Position: 395 String: TGA
Position: 408 String: TGA
Position: 448 String: TAA
Position: 505 String: TGA
Position: 512 String: TAA
Position: 621 String: TGA
Position: 700 String: TGA
Position: 722 String: TAA
Position: 743 String: TAA
Position: 752 String: TGA
Position: 857 String: TAA
Position: 864 String: TAA
Position: 957 String: TAG
Position: 974 String: TAA
Position: 1002 String: TGA
Position: 1019 String: TAA
Position: 1052 String: TGA
Position: 1198 String: TGA
Position: 1210 String: TAG
Position: 1253 String: TGA
Position: 1265 String: TAA
[download]

Observe that the script is searching after the ATG as you requested (check indexes). It looks correct to me.

Take a look and give it a try to verify it or not.

Hope this helps instead of making things more confusing.