[EMBOSS] eprimer3

[Henrikki Almusa]

On Monday 22 March 2004 23:34, Georg Otto wrote:
> Hi,
>
> I have problems using eprimer3. It seems to me that it can´t take
> multiple sequence files as an input (I tried with a multiple fasta file
> and a file in EMBL format). However primer3 itself can take multiple
> sequences. Is there something I missed?

Mail from archives:

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[EMBOSS] eprimer3: max input file number?
Date: 21.10.2003 19:41
From: Iain Drummond <idrummon at receptor.mgh.harvard.edu>

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.

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And reply to above:

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Re: [EMBOSS] maximum number of sequences for eprimer3
Date: 22.10.2003 22:06
From: Alan Bleasby <ableasby at hgmp.mrc.ac.uk>

Having had a quick look at the code I suspect that it is not
a variable involved (EMBOSS programs are designed not to be
limited in that way, usually only by system resource available).
 
The code uses pipes to redirect stdin and stdout to/from primer3_core.
A possible cause is therefore blocking from a full buffer. I'll
let the author of the eprimer3 program know about it.

HTH

Alan

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-- 
Henrikki Almusa