Re: Print A Sequence with Start codon and different Stop Codon

[choroba]

It's not clear what output you expect. To search for overlapping sequences, you can change the second group from non-grouping to a look-behind:

$sequence =~ /(ATG.*?(?<=TAA|TAG|TGA))/g

to get

ATGGTTTCTCCCATCTCTCCATCGGCATAA
ATGA

It still extracts the shortest possible sequence for each starting point (so we lost the second output).

Update: It's possible to get all the sequences without experimental regex features and depending on the return value of print like here.

my @from;
my $pos = -1;
push @from, $pos while -1 != ($pos = index $sequence, 'ATG', $pos + 1)
+;

my @to;
for my $end (qw( TAA TAG TGA )) {
    $pos = -1;
    push @to, $pos + 3 while -1 != ($pos = index $sequence, $end, $pos
+ + 1);
}

for my $f (@from) {
    for my $t (@to) {
        say substr $sequence, $f, $t - $f if $t > $f;
    }
}
__END__
Output:

ATGGTTTCTCCCATCTCTCCATCGGCATAA
ATGGTTTCTCCCATCTCTCCATCGGCATAAAAATACAGAATGATCTAA
ATGGTTTCTCCCATCTCTCCATCGGCATAAAAATACAGAATGA
ATGATCTAA
ATGA

[Anonymous Monk]

Yes, but it was so much fun :)

#!/usr/bin/perl -l

# http://perlmonks.org/?node_id=1146191

use strict;
use warnings;

my $sequence = 'AATGGTTTCTCCCATCTCTCCATCGGCATAAAAATACAGAATGATCTAACGAA'
+;

while( $sequence =~ /ATG/g )
  {
  my $rest = $';
  print 'ATG' . $` . $1 while $rest =~ /(TAG|TAA|TGA)/g;
  }

[PerlKc]

I tried that, but my output should be set of sequences with start codon ATG and end codon TAG,TAA,TGA. For example ATG...............TAA ATG...........TAG ATG.........................TGA ATG.................................TAA .......represents sequence in middle of start and stop codon

[PerlKc]

I tried that, but my output should be set of sequences with start codon ATG and end codon TAG,TAA,TGA. For example ATG...............TAA ATG...........TAG ATG.........................TGA ATG.................................TAA .......represents sequence in middle of start and stop codon I am looking for regex features to get the output. Thanks