[EMBOSS] EMBOSS eprimer3 and latest primer3_core

Peter biopython at maubp.freeserve.co.uk
Tue Apr 13 11:43:08 UTC 2010

Hello EMBOSS team,

I'm using EMBOSS 6.2.0 on Mac OS X 10.6.3 Snow Leopard:

$ embossversion
Reports the current EMBOSS version number

I need to design some primers so I wanted to try the EMBOSS tool
eprimer3, which as your documentation clearly explains requires me to
install the 'primer3' program from the Whitehead Institute
(specifically the primer3_core tool).

I downloaded and compiled the latest version of primer3, version 2.2.2
beta (using the default, i.e. just "make", which seems to be fine -
the Snow Leopard specific Makefile failed). It seems that EMBOSS
eprimer3 does not like this:

$ export EMBOSS_PRIMER3_CORE="/Users/xxx/Downloads/Software/primer3-2.2.2-beta/src/primer3_core"
$ eprimer3 fasta::lupine.nu lupine.eprimer3
Picks PCR primers and hybridization oligos
Error: Missing SEQUENCE tag

Instead, I downloaded and compiled primer3 version 1.1.4 (using the
defaults, i.e. just "make", there is no Snow Leopard specific Makefile
included) and that seems to work:

$ export EMBOSS_PRIMER3_CORE="/Users/xxx/Downloads/Software/primer3-1.1.4/src/primer3_core"
$ eprimer3 fasta::lupine.nu lupine.eprimer3Picks PCR primers and
hybridization oligos
Picks PCR primers and hybridization oligos

The eprimer3 output looks sensible too.

My guess is that something in the recent primer3 alpha and beta
releases of 2.x.x has changed since version 1.x.x and that EMBOSS
needs to be updated to cope. Is this a known issue?


Peter C.

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