test sequence

[David.Bauer at SCHERING.DE]

Hi Alan,

I wonder how the "preferred" list is created.
Restrict finds the site "CTGCAG" as recognition site of BstMAI.
This is a rather exotic enzyme, available only from one single company, which I
didn't know before.
I appologize for my ignorance if this is a common supplier in UK ;-)
On the other hand PstI is available from about 20 suppliers and this is also the
enzyme name used in various catalogue pictures of multiple cloning sites in
vectors (puc19 polylinker etc.)
So I would suggest to add the BstMAI -> PstI mapping to the distribution version
of embossre.equ.

David.




There is probably not a problem. EMBOSS only reports one
isoschizomer for cases where several REs have the same cut
site. If the  -preferred   switch is given to these
programs then the more easily available of the isoschizomers
will be reported. This is controlled by the file:

   embossre.equ

where, for each RE, you can specify which isoschizomer should be
reported.

So, first try adding -preferred. If you just want to search for
a particular set of enzymes they can be given as a comma-separated
list using the -enzymes qualifier   e.g. -enzymes "ecori bamhi"

HTH

Alan Bleasby
HGMP


PS: NEB supply an emboss-format set of files which are just the most
    common REs. You can rename them (e.g. to embossre.enz/ref/sup)
    and overwrite your current set in the emboss REBASE directory.