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Re: Epcr and primer-blast



Le Wed, Oct 10, 2018 at 11:45:38AM +0200, Andreas Tille a écrit :
> 
> I'm about to update the epcr package but its homepage[1] says:
> 
>    The e-PCR suite of tools has been retired. Please consider using
>    PrimerBLAST[2] as an alternative if you are interested in designing
>    PCR primers or identifying target sequences for your primers.
> 
>    For more information, see "Electronic-PCR (e-PCR) is retiring, use
>    Primer-BLAST instead"[3] at the NCBI Insights blog.
> 
> Please excuse my ignorance but I know nothing about primer design at
> all.  I somehow suspect that the command line tool e-PCR should now be
> replaced by a web tool (or am I missing something?  I can not find
> something inside the blast package which looks like a command line
> replacement).  Currently epcr has a popcon which is somehow "medium" in
> our Debian Med package set - so there is some relevant user base that
> is using a discontinued / replaced tool.

Hi Andreas,

a search for "primer-blast" in GitHub's repository for the NCBI C++
toolkit only returns a page containing the URL of the web service,
confirming that there does not seem to be an offline version.

In my experience, people doing large-scale primer design (where
command-line or off-line versions are definitely needed) tend to use
Primer3 directly or (more often?) through a wrapper.  Nevertheless, I
would suggest to keep the ncbi-epcr package as long as it does not have
a RC bug (which I expect to eventually as GCC continues to evolve).

Have a nice day,

Charles

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Akano, Uruma, Okinawa, Japan


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