Utility to select restriction enzymes for inverse PCR?

Henryk Bochmann bochmann-usenet0500 at gmx.net
Mon May 29 01:19:25 EST 2000

Kimberley Snowden <ksnowden at hort.cri.nz> wrote:
> Hi there,

> I would recommend looking at the average fragment size chart in the NEB
> catalogue - they give numbers for a range of different organisms. This is on
> pg 277 of the 1998/99 catalogue. It doesn't however give a comprehensive list
> of enzymes. I've done quite a bit of iPCR on plants and often find that a
> combination of two compatible enzymes (eg EcoRI + MfeI) often gives a good
> size fragment for iPCR. When in doubt, do a Southern first with a few
> different enzymes, and choose a combination with a fragment size of probably
> no more than 3 kb.

Hi Kim,

what I meant is a software or webpage which take your sequence and
return a map of restriction sites in that sequence, based on the
enzymes you select. Most of the programs I know allow you to explicitly
specify enzymes, but none allows to select by average fragment size.
I want to find out which 4-base cutters do *not* cut in my fragment,
without having to select all four-base cutters by hand.


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