Primer Design Tool Files

VERSION: 1.7

[License]:--------------------------------------------------------------------

   Copyright (C) 2010-2012  Victor Khangulov - Johns Hopkins University

   This file is part of Primer Design Tool.

   Primer Design Tool is a  free software: you can redistribute it
   and/or modify it under the terms of the GNU General Public License as
   published by the Free Software Foundation, either version 3 of the
   License, or (at your option) any later version.

   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.

   You should have received a copy of the GNU General Public License
   along with this program.  If not, see <http://www.gnu.org/licenses/>

[Creator]:--------------------------------------------------------------------

Victor Khangulov (Johns Hopkins University) vkhangulov@jhu.edu

[Project Website]:------------------------------------------------------------

https://sourceforge.net/projects/primer-design/

[Description]:----------------------------------------------------------------

This is a program to help BGME students automatically create 
primers and generate primer sheets for the database.

[System Requirements]:--------------------------------------------------------

The following requirements are describing the system that
I am currently running.  You may be able to get away with older (or newer) 
versions of packages.

Python 2.6.4
Tkinter

[Usage]:----------------------------------------------------------------------

Execute PrimerDesigner.py

Because this is a GUI (Tkinter), if you are using this over ssh, then make 
sure that the X-server is running.

[Release Notes]:--------------------------------------------------------------

2012-07-18: v1.7
* Added automatic check for updates

2012-07-16: v1.6
* Added scrollbars to the dialogs to allow for scrolling of the main windows on 
  systems where resolution cuts off visibility
* Modified handling of the deletions in the residue sequence to be generic.
  Now user can pass a string in the format: "4,5,44-49" to indicate which of the
  residues are missing in the protein sequence.

2012-07-02: v1.5, v1.4
* Fixed error when mutating to residues with a single codon, i.e. M and W

2011-10-03: v1.3
* Changed primer loc to be text not integer

2011-03-23: v1.2
* Updated license information
* Added svn keywords to the file headers
* Updated the website to point to the wiki

2011-02-08: v1.1 - Fixed bugs in v1.0
* Fixed crash when primer is designed to go past either of the protein terminals.
* Added re-sizing of the sequence text boxes to accomodate longer primers.

2011-01-31: v1.0 - First stable release
* Fixed incorrect iveralling residue display
* Changed nonspecific binding message to display True/False
* Changed default output filename to display all mutations in sequential order.

2010-11-11: v0.0.8
* Improved interface
* (Bug:3105672): Selecting other background, then regular one crashes program
* (Bug:3105674): Change glycerol stock to primer location
* (Bug:3105686): Add selection of the current codon
* (Bug:3105687): Add GC content to the summary page
* (Bug:3105689): Display residues covered on the summary page
* (Bug:3105690): Check for poly A,T,G,C
* (Bug:3105692): Implemented a check for non-specific binding
* (Bug:3105695): Add table 5 for items flagged in summary checks
* (Bug:3105694): Space added to prot seq in the output file when incomplete codon is present on the end (3').


2010-11-07: v0.0.7
Added D+VIAGLA and D+NVIAGLA backgrounds to data.in

2010-11-05: v0.0.6
Initial stable release.