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

[Fields, Christopher J]

Mark, 

I saw this has gone unanswered.  Can you post some example code so we can have a look?  Might make things go a bit faster.

chris

On Nov 27, 2013, at 2:38 PM, Mark Nadel <nadel at nabsys.com> wrote:

> I have been using Bio::Restriction::Analysis and have noticed discrepancies
> between the results on cut positions using it and some other tools.
> Checking the results by hand led me to believe that there is an error
> in Bio::Restriction::Analysis.
> (In the case of a restriction enzyme that cuts both strands, but at
> slightly different bases, the specification of which position should be
> reported is not clear, but I will try to avoid that issue in this report.)
> 
> I will use an e coli strain U00096.3 as the sequence.
> The first example will be with restriction enzyme Bpu10I with recognition
> sequence
> CCTNAGC(-5/-2) which indicates the cut on the + strand after the second C
> and on the minus strand between the T and the C opposite the A and G.
> 
> When I run this, one of the positions I get is 3449. (I've selected a case
> in which the pattern appears on the + strand). Here is a listing of the
> sequence from 3447 to 3465: CCCGTCAGCCTGAGCTTGC
> As you can see, the recognition pattern begins at 3455, and the cut on the
> + strand would be at 3456 which is what is reported by, for example
> CLCSequenceViewer. The - strand cut site would be at 3459.
> 
> Here is another example using  nicking enzyme Nt.Bpu10I that nicks only the
> + strand. The corresponding recognition sequence is CCTNAGC(-5/?). When I
> run this I get 3454 which corresponds to the beginning of the recognition
> sequence, but not the cut site.
> 
> I hope the guardians of this module will be motivated to have a look. I
> will be happy to provide any additional information that may be of use. I
> am using version 1.006901.
> 
> Thanks in advance,
> 
> Mark
> 
> 
> 
> -- 
> *Mark Nadel*
> 
> *Principal Scientist*
> Nabsys Inc.
> 60 Clifford Street
> Providence, RI  02903
> 
> Phone   401-276-9100 x204
> Fax 401-276-9122
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l