[Bioperl-l] Forward of moderated message

[Rob Edwards]

Are you sure that you are using the right module. This has been fixed 
in Bio::Restriction (ver. 1.4)

e.g.


use Bio::Seq;
use Bio::Restriction::Enzyme;
use Bio::Restriction::Analysis;
use strict;

my $seq=Bio::Seq->new(-seq=>'GTACTTTTAGAGGATGAAACCT');
my $renz=Bio::Restriction::Enzyme->new(-enzyme=>'MnII', -seq=>'^CCTC');
my $ranal=Bio::Restriction::Analysis->new(-seq=>$seq, -enzymes=>$renz);
my $enz='MnII';
my @frags=$ranal->fragments($enz);

print join "\n", @frags, "\n";


gives

GTACTTTTA
GAGGATGAAACCT

Rob


On Mar 8, 2004, at 10:43 AM, bioperl-guts-l-bounces at portal.open-bio.org 
wrote:

>
> From: Ruifang <zhangrf at xysm.net>
> Date: March 8, 2004 1:28:13 AM CST
> To: bioperl-guts-l at portal.open-bio.org
> Subject: a problem of RestrictionEnzyme
>
>
> Dear,
>
> I am a graduate student in National Lab of Medical Genetics of China.
>
> I am using Bioperl Module: RestrictionEnzyme.pm and I have encountered 
> a question about this code.
>
> I found  the restriction enzymes could not recognize the DAN sequence 
> which is reverse complement to the enzymes sequence.
> For example, the enzyme: MnlI, the recognize sequence :CCTC, the DNA 
> sequence: GTACTTTTAGAGGATGAAACCT
> the DAN sequence include  GAGG , which is reverse complement to CCTC,  
> and the MnlI should cut this sequence, but the code could not give 
> this result.
>
> May I could have answer from you soon!
>
> Thanks!
> Best Wishes!
>
> Ruifang
>
>
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