[Bioperl-l] Possible bug in Bio::Restriction::Analysis

[Mark Nadel]

Chris,

Thanks for your interest. Here is some code that will generate the data to
which I refer in my earlier post:

use Bio::DB::GenBank;

use Bio::Restriction::Analysis;

use Bio::Restriction::EnzymeCollection;


my $db = Bio::DB::GenBank->new();

my $seq = $db->get_Seq_by_acc('U00096');

my $rebase = Bio::Restriction::IO->new(

      -file   =>  '/Users/marknadel/Documents/adhoc_withrefm.txt',

      -format => 'withrefm' );

my $rebase_collection = $rebase->read();

my $ra = Bio::Restriction::Analysis->new(-seq=>$seq,-enzymes=>$
rebase_collection);

my $all_cutters = $ra->cutters;

foreach my $enz ($all_cutters->each_enzyme()){

print("\n");

print($enz->name());

print("\n");

 my @z=  $ra->positions($enz->name());

    my $k = $#z;

    for ($j=0;$j<=$k;$j++){

    print "\t$z[$j]";

   }

}

print "\nDONE";


Unfortunately, the enzymes that I mentioned in the post are not included in
the base distribution. Here is a very brief file to use:

<1>Nt.Bpu10I

<2>

<3>CCTNAGC(-5/?)


<1>Bpu10I

<2>BpuDI

<3>CCTNAGC(-5/-2)

<4>?(5)

<5>Bacillus pumilus 10

<6>NEB 1777

<7>FINV

<8>Degtyarev, S.K., Zilkin, P.A., Prihodko, G.G., Repin, V.E., Rechkunova,
N.I., (1989) Mol. Biol. (Mosk), vol. 23, pp. 1051-1056.

Stankevicius, K., Lubys, A., Timinskas, A., Vaitkevicius, D., Janulaitis,
A., (1998) Nucleic Acids Res., vol. 26, pp. 1084-1091.

This is the file /Users/marknadel/Documents/adhoc_withrefm.txt used in the
snippet above.

Thanks again,

Mark

-- 
*Mark Nadel*

*Principal Scientist*
Nabsys Inc.
60 Clifford Street
Providence, RI  02903

Phone   401-276-9100 x204
Fax 401-276-9122