Protocol Online logo
Top : New Forum Archives (2009-): : BioForum Method Discussion Archives

parse primer3 output - (Mar/26/2004 )


I've obtained a primer3 output file from a batch primer3 run. The file is a bit unwieldy and picking out the fields of interest by copy/paste into a spreadsheet seems like a pain. Does anyone know of a simple perl script (or anything else) that will parse the primer3 output file into a table or tab delimited format?

Thanks in advance,



Hi Eric,

you may have a look on to see if you can find a ready-to-use primer3 parser.

If there is not, I don't think you can find one that meets your specific needs. In that case I may write some code for you depending on the complexity of the task. You can give me a sample primer3 result and your desired output.



I'll look around bioperl and see what I can find. Thanks for the offer - if I can't find anything already written I'll just find someone here at my University to give the script a go. That's how I ended up getting around my earlier problem of limiting my primer search to the 3' end of my sequences. But thanks again for your quick responses and offer to help.




You might also want to check out AutoPrime at You could get the code for batch prcessing, but you can also use the comfortable web-GUI for single searches...

Cheers, Flexer