==================================Application===================================
CEMAsuite
==================================Requirements==================================
Java 1.7 or higher
====================================Package=====================================
edu.lsu.csv2
=====================================Author=====================================
Courtney E. Lane
=====================================Notes======================================
-Example alignments can be found in resources folder.
-User Manual and Screenshots files (PDF) can be found in the help folder.
==================================Description===================================
The intent of CEMAsuite is to aid in the design of a sort of
minimum-degeneracy consensus primer set. This application allows for a balance
of specificity and sensitivity in a primer set.
This application addresses this problem by starting with a protein MSA,
where the likelihood of "true" conservation is higher and generating a
codon-equivalent multiple alignment (CEMA) using the coding sequence of each
protein sequence within the protein MSA. Next, it enables the user to quickly
and effectively score each position within the alignment using one of multiple
scoring algorithms in order to assign a quality to each position. The Primer3
primer design program can then accept both the consensus sequence for this CEMA
and the quality scores assigned to each position and design high-quality
consensus primers. Selective degeneracy can be added by the user until the
calculated stability of each primer-template pair is acceptable. This
application also attempts to condense the vast amounts of information usually
associated with MSAs into formats which are intuitive and discernible.
===================================Change=Log===================================
Version 2.0.9
*Separated PlotPainter and Plot classes.
*Added preview window for saving quality plot.
*Added option to paint background with png quality plot.
Version 2.0.8
-Allow editing and restoration of Primer3 settings (p3_settings_file)
via settings menu.
*Default values can be set from v1.1.4, web v0.0.4, web v3.0.0, and
web v4.0.0.
*Settings can be adjusted via Settings>Primer3>Edit Current Settings
*Values can be reset to desired default, or a new default settings
file can be chosen. These actions will reset current default
Primer3 settings.
-Better control over inputs for save plot prompt.
-Added document flag indicator panel for hybridization output.
*Location of flagged sets will be indicated by color using a small
panel representing the entirety of the document on the right hand
side.
*Clicking panel will update view to specified location relative to
the document.
-Complete synchronization of Primer3.
Tested on OSX 10.9.4 with Java 1.7.
-Added wrapper class to check for proper Java version.
Version 2.0.7
-Sped up hybridization process.
-Corrected primer3 IO primer index bug.
-Updated divergent primer warnings.
Version 2.0.6
-Incorporated automated version/build handling.
Values stored in version.properties file. Subversion numbers must
be updated through manual ant calls of build.xml targets. Build
number updates automatically during "-post-jar" target.
-Cached nucleic degenerate comparisons.
Version 2.0.5
-Brought back color sliders to hybridization input panel with
ColorSliderUI class.
-Added DNAToolKit.
*Allows for quick permutation of degenerate DNA sequences
(complement, reverse, reverse complement)
*Allows for translation of non-degenerate DNA sequences (all
tables, 3 orfs)
*Allows for quick FASTA formatting of degenerate DNA sequences
(variable line length, max 80 chars)
-Added DNAToolKit popup menu to CEMA sequence alignment text area.
-More Primer3 error handling.
-Mac Primer3 user permissions handling.
-Added HTML export for hybridization output.
-Incorporated more accession formats (Genbank WGS, MGA).
Version 2.0.4
-Minor edits to UI. (hover for details, no primers found please try
again.)
-Organism builder protein/cds length checks provide more useful
information.
-Efetch organism builder allows for omission of erred sequences and
continuing of analysis.
Version 2.0.3
-Incorporated MacOS compatible Primer3 binary.
-Adjusted UI errors for MacOS compatibility issues.
Version 2.0.2
-Fixed typo in amino acid name.
-Prevention of Primer3 submission attempts when not on Windows machine.
Version 2.0.1
-Modified accession to accept protein/nucleic acid context to improve
parsing.
-Modified hybridization algorithm to reduce redundant calculations.
-Corrected SantaLucia & Hicks entropic adjustment citation.
-Fixed axis length rendering issue with plot.
Version 2.0
-Initial distribution.
==================================Installation==================================
No real installation involved (yet). Single executable .jar file
(CEMAsuiteV2.jar) which can be run on double-click, or by commanding "java.exe
jar CEMAsuiteV2.jar" from the CEMAsuiteV2.jar file's directory.
In other words, go to your console/terminal and type "cd <path of folder
holding CEMAsuite.jar file>" and hit enter. Then, type "java.exe jar
CEMAsuiteV2.jar" and hit enter again.
An icon file is included within the distribution if it is desired to create
a shortcut.
