[EMBOSS] restrict -limit

[ajb at ebi.ac.uk]

Hello Aengus,

Restrict will report enzymes with the same recognition site
if the source REBASE database lists them as having different
cut sites. That appears to be the case with your reported output.
So, you do seem to be using it correctly and the results also seem to
be correct.

Alan


>
> I seem to be having trouble with restrict not picking up -limit or am I
> not using it correctly?
>
> I shouldnt be getting both BssKI and ScrFI should I or indeed both BseBI
> and EcoRII ???
>
> ########################################
> # Program: restrict
> # Rundate: Wed  5 Dec 2007 13:17:08
> # Commandline: restrict
> #    -sitelen 4
> #    -enzymes all
> #    -limit
> #    -blunt
> #    -single
> #    [-sequence] rs9584819.ff
> #    -outfile
> /home2/bioadmin/projects/MANOJ/RESTRICT_RESULTS/rs9584819.ff.restrict
> # Report_format: table
> # Report_file:
> /home2/bioadmin/projects/MANOJ/RESTRICT_RESULTS/rs9584819.ff.restrict
> ########################################
>
> #=======================================
> #
> # Sequence: rs9584819     from: 1   to: 101
> # HitCount: 24
> #
> # Minimum cuts per enzyme: 1
> # Maximum cuts per enzyme: 1
> # Minimum length of recognition site: 4
> # Blunt ends allowed
> # Sticky ends allowed
> # DNA is linear
> # Ambiguities allowed
> #
> #=======================================
>
>    Start     End Enzyme_name Restriction_site 5prime 3prime 5primerev
> 3primerev
>       13      17 BssKI       CCNGG                12     17         .
>    .
>       13      17 BseBI       CCWGG                14     15         .
>    .
>       13      17 ScrFI       CCNGG                14     15         .
>    .
>       13      17 EcoRII      CCWGG                12     17         .
>    .
>
>
>
>
> Regards
> Aengus
>
>
>
> --
> -----------------------------------------------------------------------
> Aengus Stewart
> Head of Bioinformatics and BioStatistics
> Bioinformatics and BioStatistics               Tel: +44 (0)20 7269 3679
> Cancer Research UK, Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK
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