use strict;
use warnings;

my $string='YYSFTVMETDPVN[115]HMVGVISVEGRPGLFWFN[115]ISGGDK';
my $offset = 0;
my $substring = 'N[115]';
my @positions;

while (1) {
    my $pos = index($string, $substring, $offset);
    last if $pos < 0;
    push @positions,$pos;
    $offset = $pos + length($substring);
}

print "Positions: @positions\n";
[download]

Positions: 12 35
[download]

Thanks for the reply!
But, if you look at the string, I just want the position of 'N', without taking into consideration the [115] thing. In the code, you provided, it works ok for the first 'N', but for the second 'N', the correct position is 30 and not 35(this is because you count the first [115] and this increases the length of the string.

OK. I said I didn't understand what you meant! How about this then (damn the hard-coded 5):

use strict;
use warnings;

my $string='YYSFTVMETDPVN[115]HMVGVISVEGRPGLFWFN[115]ISGGDKN[115]';
my $offset = 0;
my $substring = 'N[115]';
my @positions;

while (1) {
    my $pos = index($string, $substring, $offset);
    last if $pos < 0;
    $offset = $pos + length($substring);
    
    $pos -= 5 * @positions;
    push @positions,$pos;
}

print "Positions: @positions\n";
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Gives:

Positions: 12 30 37
[download]

I added another N for testing.

Update:I have recieved a /msg puzzling about a line of code. Here is a description of $pos -= 5 * @positions;
We need to adjust the position by the length of [115] (5 characters), not just just once but for each position found. I use @positions in scalar context to get me the number of elements (scalar context is forced by the multiplication operator *). The first time around the loop the number of elements in @positions is zero, so $pos is not decremented. Subsequently it is decremented by 5 * number-of-items-found.

How about using split rather than index? Using cdarke's extended data shows that you have to use a third argument to split of -1 to allow the trailing empty element if the split term is at the end of the line.

$ perl -le '
> $str = q{YYSFTVMETDPVN[115]HMVGVISVEGRPGLFWFN[115]ISGGDKN[115]};
> @chunks = split m{(?<=N)\[115\]}, $str, -1;
> $posn = -1;
> print $posn += length for @chunks[ 0 .. $#chunks - 1 ];'
12
30
37
$
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I hope this is of interest.

 perl -e '$_="YYSFTVMETDPVN[115]HMVGVISVEGRPGLFWFN[115]ISGGDK"; /N(?=\
+[115\])(?{print pos, "\n"})(*FAIL)/'
13
36
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>perl -wMstrict -le
"sub substr_offsets {
   my ($str, $substr, $subst) = @_;
   $subst = qq{\0} unless defined $subst and length $subst;
   die qq{substitution string '$subst' found in '$str'}
     if $str =~ m{\Q$subst\E}xms;
   die 'substring same as substitution string'
     if $substr eq $subst;
   $str =~ s{ \Q$substr\E }{$subst}xmsg;
   my @offsets;
   $str =~ s{ \Q$subst\E }{ push @offsets, pos $str }xmsge;
   return @offsets;
   }
 for (@ARGV) {
   my @offsets = substr_offsets($_, 'n[115]');
   print qq{string: '$_';  offsets: (@offsets)};
   }
"
""  a  ab  n[115]  An[115]  n[115]A
n[115]n[115]  n[115]n[115]n[115]
An[115]n[115]n[115]  n[115]n[115]n[115]A
01234n[115]012345n[115]n[115]
string: '';  offsets: ()
string: 'a';  offsets: ()
string: 'ab';  offsets: ()
string: 'n[115]';  offsets: (0)
string: 'An[115]';  offsets: (1)
string: 'n[115]A';  offsets: (0)
string: 'n[115]n[115]';  offsets: (0 1)
string: 'n[115]n[115]n[115]';  offsets: (0 1 2)
string: 'An[115]n[115]n[115]';  offsets: (1 2 3)
string: 'n[115]n[115]n[115]A';  offsets: (0 1 2)
string: '01234n[115]012345n[115]n[115]';  offsets: (5 12 13)
[download]

A solution that uses index and substr.

$ perl -le '
> $str = q{YYSFTVMETDPVN[115]HMVGVISVEGRPGLFWFN[115]ISGGDKN[115]};
> $posn = -1;
> while ( ( $posn = index $str, q{N[115]}, $posn ) > -1 )
> {
>     print +( $posn ++ );
>     substr $str, $posn, 5, q{};
> }'
12
30
37
$
[download]

Making the solution more general and avoiding modifying the original string.

$ perl -Mstrict -wle '
> print for findPosns(
>    q{YYSFTVMETDPVN[115]HMVGVISVEGRPGLFWFN[115]ISGGDKN[115]},
>    q{N},
>    q{[115]}
>    );
> 
> sub findPosns
> {
>     my ( $str, $textKeep, $textThrow ) = @_;
> 
>     my $text  = $textKeep . $textThrow;
>     my $len   = length $textThrow;
>     my @posns = ();
>     my $posn  = -1;
>     while ( ( $posn = index $str, $text, $posn ) > -1 )
>     {
>         push @posns, $posn ++;
>         substr $str, $posn, $len, q{};
>     }
>     return @posns;
> }'
12
30
37
$
[download]

I hope this is useful.

I wondered what would happen if other letters had square bracketed numbers, I solved that in this way. Seems a regex is the "wrong" solution but it was what struck me first.

use strict;
use warnings;

my $string='YYSFTVME[13]TDPVN[115]HMVGVISVE[13]GRPGLFWFN[115]ISGGDKN[1
+15]';
my $substring = 'N[115]';

my @chars = $string =~ /(.(?:\[\d+\])?)/gxms;

my @positions;
foreach my $i (0..$#chars) {
    push @positions, $i if $chars[$i] eq $substring;
}

print "Positions: @positions\n";
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#!/usr/bin/perl
use strict;

my $string = 'YYSFTVMETDPVN[115]HMVGV'
           . 'ISVEGRPGLFWFN[115]ISGGDK';
my @pos;
my $test = 'N[115]';

for ( my $i = 0; $i < length( $string ); $i++ ) {
    push( @pos, $i )
      if ( substr( $string, $i, 6 ) eq $test );
}

@pos = map { $_ == 0 ? $pos[$_] : $pos[$_] - 5 } (0 .. $#pos );
print "Found N at positions: ". join( ', ', @pos ), "\n";
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