[EMBOSS] problems with eprimer3

[ajb at ebi.ac.uk]

Hello Felipe,

Thanks for the reminder of this. Downloading the developer's version
will not help.

A version of eprimer3 that should work with primer3 2.x.x can
be downloaded from:

  http://www.ebi.ac.uk/~ajb/eprimer3/eprimer3.c

if you're desperate. Note that it hasn't been tested very recently and is
not, as yet, official. We are still debating how to deal with
new and old versions of primer3. An odd hindrance
is, given that it would be useful to keep the
1.x.x version around for compatibility reasons, what to call them.

If you choose to try the above then any feedback would be welcome.

ATB

Alan



> Dear EMBOSS developers and users,
>
> I am having some problems with the eprimer3 application in EMBOSS. I
> have been using primer3 online (primer3plus, ncbi site) with good
> results, and I just tried using it in EMBOSS. I am using MacOS 10.6.4
> (Snow Leopard), with EMBOSS 6.3.1 installed by Fink (an UNIX porting
> system for MacOS). The primer3 version is 2.2.3.
>
> One of the problems has already being described in this list, but it
> seems to still be around. When I call eprimer3 with a sequence, the
> output is:
> Picks PCR primers and hybridization oligos
> Error: Missing SEQUENCE tag
>
> See this thread for details, I did the same tests and the results were
> similar; primer3_core is OK, but it seems that eprimer3 has not been
> updated yet to successfully communicate with the primer3_core 2.x
> versions:
> http://www.mail-archive.com/emboss@lists.open-bio.org/msg01405.html
>
> I have not tried yet the developer's version of EMBOSS, should I?
>
> Regards,
>
> --
> --------------------oOo--------------------
> Felipe Martínez-Pastor, Ph. D.
> ITRA-ULE (Research in Assisted Reproductive Technologies)
> INDEGSAL (edificio Biomedicina)
> University of León
> Campus de Vegazana
> 24071-León (Spain)
> Office phone: +34 987 291 000 + 5679
> Fax:          +34 987 291 282
> Mobile:       +34 687 365 362
> e-mail: felipe.martinez at unileon.es
>          f.martinez.pastor at gmail.com
> website: http://itra.unileon.es
> -------------------------------------------
>
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