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<FONT FACE="Verdana"><SPAN STYLE='font-size:12.0px'>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 “sleeping” 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.<BR>
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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). <BR>
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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 returned.<BR>
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Does anyone know if there is a config file that would change the behavior of eprimer3, or is this a bug in the program?<BR>
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Iain Drummond, Ph.D.<BR>
Assistant Professor<BR>
Department of Medicine, Harvard Medical School and <BR>
Renal Unit, Massachusetts General Hospital <BR>
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idrummond@partners.org<BR>
idrummon@receptor.mgh.harvard.edu<BR>
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Lab Home Page:<BR>
<a href="http://danio.mgh.harvard.edu">http://danio.mgh.harvard.edu</a><BR>
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