$protein='acgtacgt';
#suppose this is my string. i want to find the position of the 2nd cg which occurs in this string

$pos=index($protein,'cg')+2;
#i m using this program to find second  position of the motif but it is not working

or can u please tell me some other way of finding the position of the second cg

I'm not sure if you are asking the right question or using a good example, but for the string you posted, you can use rindex instead  of index:


$motif = 'cg';
$protien = 'acgtacgt';
$pos = rindex $protien,$motif;
print $pos;


which returns the position of the last occurance of the substring. Now if the sting can be like this:

$protien = 'acgtacgtatacgtt';

rindex will not work to find the second occurance of the substring. You have to index the string twice using the first position + the length of the substring:


my $motif = 'cg';
my $protien = 'acgtacgtatacgtt';
my $first_pos = index  $protien,$motif;
my $second_pos = index $protien, $motif, length($motif)+$first_pos;
print $second_pos;






I forgot about the pos() function which could be also, but since it uses a regular expression it might be less efficient than above suggestions:


my $motif = 'cg';
my $protien = 'acgtacgtatacgtt';
while($protien =~ /$motif/g){
   print +(pos($protien) - length($motif)),"\n";
}


the + is in there only so the print function prints the \n on the end, it's not doing anything else.

thank you sir for your reply
the previous solution worked.

Thank you for your feedback. For me it is important to know that the help I give is useful and that it is being taken into consideration, otherwise I will stop helping people that never reply to suggestions I offer. That is my own personal policy, nothing to do with this website or Graham.

---