Bio.Emboss.Primer3 module

Code to parse output from the EMBOSS eprimer3 program.

As elsewhere in Biopython there are two input functions, read and parse, for single record output and multi-record output. For primer3, a single record object is created for each target sequence and may contain multiple primers.

i.e. If you ran eprimer3 with a single target sequence, use the read function. If you ran eprimer3 with multiple targets, use the parse function to iterate over the retsults.

class Bio.Emboss.Primer3.Record

Bases: object

Represent information from a primer3 run finding primers.


  • primers - list of Primer objects describing primer pairs for this target sequence.

  • comments - the comment line(s) for the record


Initialize the class.

class Bio.Emboss.Primer3.Primers

Bases: object

A primer set designed by Primer3.


  • size - length of product, note you can use len(primer) as an alternative to primer.size

  • forward_seq

  • forward_start

  • forward_length

  • forward_tm

  • forward_gc

  • reverse_seq

  • reverse_start

  • reverse_length

  • reverse_tm

  • reverse_gc

  • internal_seq

  • internal_start

  • internal_length

  • internal_tm

  • internal_gc


Initialize the class.


Length of the primer product (i.e. product size).


Iterate over primer3 output as Bio.Emboss.Primer3.Record objects.

Parse primer3 output into a Bio.Emboss.Primer3.Record object.

This is for when there is one and only one target sequence. If designing primers for multiple sequences, use the parse function.