Bio::Seq::PrimedSeq

Bio::Seq::PrimedSeq is a software that represents a sequence along with two primers surrounding a target region. This module was created to address the need for a more comprehensive way to represent the primer-sequence complex.

To use this software, there are two suggested methods. The first method involves obtaining the output from Bio::Tools::Run::Primer3, Bio::Tools::Primer3, or Bio::Tools::PCRSimulation. After obtaining the output, a fasta file is used to design some primers using Primer3. Then, a file is created to store the resulting annotated sequences.

The second method involves creating a genbank file for a sequence and its cognate primers. This requires a sequence file with the template and two primers that match it in fasta format. After reading the three sequences, the primed sequence object is set up, and a file is created for output. The final step is to print out the sequence, which should produce a genbank file with labeled primers.

In summary, Bio::Seq::PrimedSeq is a useful software for representing a primer-sequence complex. It offers two different methods for using the software and provides a more comprehensive way to represent these important genomic elements.