[EMBOSS] eprimer3: max input file number?

Iain Drummond idrummon at receptor.mgh.harvard.edu
Tue Oct 21 16:41:06 UTC 2003

I have run into a limitation using eprimer3 as an interface for primer3. It
seems that eprimer3 will accept up to 23 sequences (in a single fasta
formatted text file) but not 24 or more; with 24 or more sequences, eprimer3
and primer3_core will just hang as ³sleeping² processes and never finish. My
goal is to automate genomic sequence analysis (zebrafish) in order to
generate new, potentially useful polymorphic markers from dinucleotide
repeats. eprimer3 is the last step where a long list of ~500 bp sequences
are sent to primer3 to make primers.

I run into this problem both on a Sun ultra5 running solaris 8 (1GB ram) and
on a mac G4 running OS X 10.2.8  (640 MB ram).

To see whether the problem was in primer3_core or eprimer3, I prepared a
list of 30 and 60 short sequences in Boulder io format and submitted them
directly to primer3_core; no problem there, 30 or 60 primer pairs were

Does anyone know if there is a config file that would change the behavior of
eprimer3, or is this a bug in the program?

Iain Drummond, Ph.D.
Assistant Professor
Department of Medicine, Harvard Medical School and
Renal Unit, Massachusetts General Hospital

idrummond at partners.org
idrummon at receptor.mgh.harvard.edu

Lab Home Page:

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