[EMBOSS] maximum number of sequences for eprimer3

Iain Drummond idrummon at receptor.mgh.harvard.edu
Wed Oct 22 18:03:49 UTC 2003

Hi Sebastian,

Interesting that you see the same problem with eprimer3 but the cutoff
number varies; I wonder what the key variable is.

I have used primer3 (primer3_core) and that has no cutoff; all the sequences
are processed. I was hoping to use eprimer3 because the input and output
files are easier to manage; I have limited perl scripting skills and I was
trying to avoid converting the input to Boulder io format which for me would
be laborious.


I've been looking at the files you sent to me. Now I realize that I always
used primer3, not eprimer3 and the input file is in different format. Anyway
I made the test (with eprimer3) and the cut off value seems to be 10
sequences (more than that end into a sleep process). A workaround would be
to send the job to eprimer3 in batch with the size it can handle. This will
not correct the problem but at least you could get te results.
Have you tried with the primer3 instead of eprimer3?
Sebastian Bassi.
Advanta Seeds. Balcarce Research Station.

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