[Bioperl-l] Restriction Enzyme cuts on Circular plasmids

[Gray, John]

Sorry, the code I pasted in my last email was missing some hard returns.  It should have looked like this:

## Make circularity function properly AGAIN!!
## $concat is set to the length of the recognition sequence -1 
$concat = 5; 
$sequence = uc ($& . (substr $sequence, 0, $concat-1));

The additional sequence must then be later removed from the appropriate fragment.  (Here I am only after the length of the fragments):

## Cut the sequence with the restriction enzyme object. 
@fragments = eval{ $re->cut_seq($seq); }; 
$@ && die "\n*** TROUBLE CUTTING:\n$@\n"; 

## pull lengths from array of sequences
my @fraglen;
my $i = 0;
foreach (@fragments) {
        $fraglen[$i] = length $_;
        $i++;
        }
## Sum first and last fragment lengths due to circularity, remove last 
$fraglen[0] = $fraglen[0] + $fraglen[@fraglen-1] - $concat; 
pop @fraglen;



-------------------------------------------------------------------------------------
John T. Gray, Ph.D.
Director, Vector Development & Production
Experimental Hematology Division
Hematology-Oncology
St. Jude Children's Research Hospital
D2038A, Mail Stop 341
332 N. Lauderdale Street
Memphis, TN 38105 
(901) 495-4729 phone
(901) 495-2176 fax
John.Gray at stjude.org