PRIMERVIEW version 3.0

Author: Damien O'Halloran, The George Washington University

Installation

1. Download and extract the primerview.zip file
   tar -xzvf primerview.zip
2. The extracted dir will be called PRIMERVIEW

  cd PRIMERVIEW  
  perl Makefile.PL  
  make  
  make test  
  make install 

Getting Started

1. You must have muscle.exe in your PATH
   Click here to get MUSCLE
2. You must have primer3 in your PATH
   Click here to get primer3
3. Must have following BioPerl modules:
   Bio::SeqIO
   Bio::Tools::Run::Alignment::Muscle
   Bio::AlignIO
   Bio::Align::Graphics
   Bio::Graphics
   Bio::SeqFeature::Generic
   WARNING: the subroutine 'clean_up' deletes the '.fa', '.fa.fasta', and '.fa.fasta.aln' extension files generated from cwd
4. Start with a sequence file in FASTA format (for example see test_seqs.fasta)

Usage

Run as follows:

  use strict;
  use warnings;
  use PRIMERVIEW;

  my $in_file = "test_seqs.fasta";

  my $tmp = PRIMERVIEW->new();
 
   $tmp->load_selections(  
      in_file         => $in_file, 
      single_view     => "1",   
      batch_view      => "1",      
      clean_up        => "1"   
   ); 
   
   $tmp->run_primerview();  

Contributing

All contributions are welcome.

Testing

PRIMERVIEW was successfully tested on:

• [x] Microsoft Windows 7 Enterprise ver.6.1
• [x] Linux Ubuntu 64-bit ver.16.04 LTS

Support

If you have any problem or suggestion please open an issue here.

License

GNU GENERAL PUBLIC LICENSE