FAS-DPD - Family Specific Degenerate Primer Design tool Version 1.4.3

Date: 2021-12-17

Released under the terms of the General Public License Version 3 (GPL v3) See the file LICENCE for details.

General

FAS-DPD core searching and scoring algorithms is working correctly. Several features will be added in future versions.

Authors

FAS-DPD project, including algorithms design, software implementation and experimental laboratory work, is being developed as a part of the Research Program:

• "Microbiología molecular básica y aplicaciones biotecnológicas" ( Basic Molecular Microbiology and biotechnological applications)

And is being conducted at:

• LIGBCM: Laboratorio de Ingeniería Genética y Biología Celular y Molecular. (Laboratory of Genetic Engineering and Cellular and Molecular Biology) Universidad Nacional de Quilmes.(National University Of Quilmes) Quilmes, Buenos Aires, Argentina.

The complete team for this project is formed by:

• ph.D. Javier A. Iserte.
• ph.D. Betina I. Stephan.
• ph.D. Sandra E. Goñi.
• ph.D. P. Daniel Ghiringhelli.
• ph.D. Mario E. Lozano.

Corresponding Authors

• Javier A. Iserte. [email protected]
• Mario E. Lozano. [email protected]

Requisites

• Java JRE 15.
• JUnit 5 - http://sourceforge.net/projects/junit.

Running FAS-DPD

FAS-DPD is executable from command line. See 'examples' folder and Documentations for details.

Documentation

Api documentation produced with javadoc is found in 'doc' folder. Manual with instructions to use FAS-DPD are in file: 'MANUAL'

Package contents

/src/         : Code source files.
/examples/    : Example showing how to use FAS-DPD.
/doc/         : API documentation.
/lib/         : Contains cmdGetArg_2.1.2.jar - Library for command line
                parsing.
StandardCode  : File containing the standard genetic code used in FAS-DPD.
LICENCE       : GPL v3 license terms.
CHANGELOG     : Log with version modifications.
VERSION       : Version.
MANUAL.md     : FAS-DPD manual.
Readme.md     : This file.

Bug report

Please send a mail to Javier Iserte [email protected] including thedetails of bugs.

Setting up development enviroment.

JDK

You will need the JDK-15.

Dependencies

This is a small project with unmanaged dependencies. There are two dependencies required for this project.

• cmdGetArg library: It comes included within the source code.
• Junit 5: You can download junit-platform-console-standalone-1.8.2.jar from maven central and put it in the lib folder. Then update .classpath file.