restriction mapping

Peter Rice peter.rice at
Tue Oct 8 13:30:31 UTC 2002

Mike Quail wrote:
> I am currently looking to isolate restriction fragments that cover gaps 
> that are left in several genomes. To do this I need to cut the sequence 
> we have of a genome with all known database enzymes and then select 
> those that just cut a few times and in the right place so as to excise 
> the region of the genome I require.
> Have you any ideas of how this could be done in EMBOSS.

You just need to know the enzymes that only cut twice, for example?

% restrict -min 2 -max 2 -plasmid

(the -plasmid may look odd, but it means "circular DNA" and says nothing 
about the size :-)

You can also check each enzyme one at a time afterwards:

% restrict -plasmid -fragment -enzyme BssHI

... the -fragment option includes the fragment sizes at the end of the 
report. You will need the positions and the fragment sizes to choose an enzyme.

You can select other report formats (-rformat), but the default is probably 
the most useful for your case (-rformat EMBL or GFF, for example, will miss 
the -fragment output)

Meanwhile, a graphical view could be nice so you can look for restriction 
sites on screen.
We can look into that.

Hope this helps,

Peter Rice

Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at +44 1223 224723

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