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Abstract
BackgroundComplex PCR applications for large genome-scale projects require fast, reliable and often highly sophisticated primer design software applications. Presently, such applications use pipelining methods to utilise many third party applications and this involves file parsing, interfacing and data conversion, which is slow and prone to error. A fully integrated suite of software tools for primer design would considerably improve the development time, the processing speed, and the reliability of bespoke primer design software applications.ResultsThe PD5 software library is an open-source collection of classes and utilities, providing a complete collection of software building blocks for primer design and analysis. It is written in object-oriented C++ with an emphasis on classes suitable for efficient and rapid development of bespoke primer design programs. The modular design of the software library simplifies the development of specific applications and also integration with existing third party software where necessary. We demonstrate several applications created using this software library that have already proved to be effective, but we view the project as a dynamic environment for building primer design software and it is open for future development by the bioinformatics community. Therefore, the PD5 software library is published under the terms of the GNU General Public License, which guarantee access to source-code and allow redistribution and modification.ConclusionsThe PD5 software library is downloadable from Google Code and the accompanying Wiki includes instructions and examples: http://code.google.com/p/primer-design
Highlights
As experimental DNA sequence manipulations become increasingly complex and large scale genome engineering projects are planned, software is needed for the design and in silico evaluation of oligonucleotide primers that satisfy complex criteria
Software packages currently available are most suited for the design of primer pairs for individual PCR applications
The development time can be reduced considerably by a modular method using reusable primer design components from a tried and tested software library, which can be employed in the final primer design system
Summary
As experimental DNA sequence manipulations become increasingly complex and large scale genome engineering projects are planned, software is needed for the design and in silico evaluation of oligonucleotide primers that satisfy complex criteria. Experimental procedures involving multiple sequential PCR steps often require more complex analysis, which is time consuming and error prone using the currently available programs. The development time can be reduced considerably by a modular method using reusable primer design components from a tried and tested software library, which can be employed in the final primer design system. Complex PCR applications for large genome-scale projects require fast, reliable and often highly sophisticated primer design software applications. Such applications use pipelining methods to utilise many third party applications and this involves file parsing, interfacing and data conversion, which is slow and prone to error. A fully integrated suite of software tools for primer design would considerably improve the development time, the processing speed, and the reliability of bespoke primer design software applications
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