Okay, I think understand now. I also think that the following code should do what you want. It takes a sequence ($seq) and a motif (@motif, which may be degenerate) and finds all the matches of greater than 3 residues.

Again, this may be a suboptimal solution and I can't shake the nagging feeling that there's a simpler way.

Of course, that describes all my perl experiance to date :-)

Apologies to all and sundry for once again descending into biological jargon. It's the only way I can get my head round this stuff...

#!/usr/bin/perl -w

use strict;
use warnings;

my $seq="APKLGIYSPRIGLYHFHKLDTPRLGAKLJHHDGFYSDA";
my @motif=("ST","P","RK","ILVF","G","ILVFM","Y");

# set up motif array of arrays

my @motifarray; 
for (my $e=0;$e<=$#motif;$e++){
    my @elementarray= split (/ */, $motif[$e]);
    $motifarray[$e]=\@elementarray;
}

my $mstartpos = 0;  # starting point within motif 
my $success = 0;

# cycle through starting motif residues ("ST","P" etc.)

MOTIFRES: while ($mstartpos+1 < $#motif){
    
    # find all matches for a given starting motif residue

    my $test=$seq;
    my $lastmatchpos=0;
    while ($lastmatchpos < length($seq)){
        my $found='';

        # deal with the first 3 residue matches as a special case

        my @r0=@{$motifarray[$mstartpos]};   
        my @r1=@{$motifarray[$mstartpos+1]};
        my @r2=@{$motifarray[$mstartpos+2]};   
        if ($test=~ /([@r0])(?=[@r1][@r2])/gc){
            $found = $1;
            $lastmatchpos=pos($test);
        }

        # next motif starting residue if no further matches found

        unless ($found){
            $mstartpos++;
            next MOTIFRES;
        }
        
        # get all the other residues in the motif
        
        for (my $e=$mstartpos+1;$e<=$#motifarray;$e++){
            my @rn=@{$motifarray[$e]};
            if ($test=~ /\G([@rn])/gc){
                $found .= $1;
            }
        }

        # print out what we've got so far
        $success++;
        print ("$found at $lastmatchpos\n");
     }

    # repeat, using the next motif residue as the new starting point
    
    $mstartpos++;
}

die ("No matches found.\n") unless ($success);
print ("Total number of matches (nested or otherwise): $success\n");
[download]

Have fun,
Tim

Update: Minor bugfix; also removed a couple of superfluous and misconceived lines to tidy it up a bit.

---

---

• Are you posting in the right place? Check out Where do I post X? to know for sure.
• Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:

  <code> <a> <b> <big> <blockquote> <br /> <dd> <dl> <dt> <em> <font> <h1> <h2> <h3> <h4> <h5> <h6> <hr /> <i> <li> <nbsp> <ol> <p> <small> <strike> <strong> <sub> <sup> <table> <td> <th> <tr> <tt> <u> <ul>

• Snippets of code should be wrapped in <code> tags not <pre> tags. In fact, <pre> tags should generally be avoided. If they must be used, extreme care should be taken to ensure that their contents do not have long lines (<70 chars), in order to prevent horizontal scrolling (and possible janitor intervention).
• Want more info? How to link or How to display code and escape characters are good places to start.