A Workflow-based High Throughput Toolkit for Primer Design
Lead Research Organisation:
Aberystwyth University
Department Name: Computer Science
Abstract
The Polymerase Chain Reaction (PCR) is one of the core techniques of biotechnology. The technique allows the amplification of sections of DNA. This is useful in a wide variety of genetic manipulation or validation techniques. Primers are strands of nucleic acid that are used as starting points for the amplification in PCR. Primers must be designed to meet certain biological and physical constraints, in order that the reaction will succeed. The design constraints are complex enough that the software is needed to help biologists design efficient primers. Existing primer design software is not flexible enough to meet the ever more ambitious requirements of novel applications of PCR. For example, some applications of PCR may involve many primers concurrently, or staged reactions where primers are first used independently, and then joined as chimeras. We propose to develop a new primer design software toolkit that will meet the requirements of 21st century biotechnology. This will be flexible and extensible, and provide a library of components that can be put together in multiple combinations, coordinated by complex workflows, and available for programmers to use in automated environments. This toolkit will be made available as open source for bioinformaticians to tailor to the specific purposes of their laboratories.
Technical Summary
The Polymerase Chain Reaction (PCR) is one of the core techniques of biotechnology. Software to design primers is required for the efficient application of PCR. Existing primer design software is not flexible enough to meet the ever more complex requirements of novel applications of PCR. We propose to develop a new primer design toolkit that will meet the requirements of 21st century biotechnology. We need a primer design toolkit that is a flexible and extensible collection of components that can be put together in multiple combinations, coordinated by complex workflows, and available for programmers to use in automated environments. Our proposed toolkit will be open-source. We will follow standard software engineering methodology, including a detailed specification stage using tools such as UML, workflow languages and Haskell. We will also provide an evaluation, against the specification and against other primer design tools. The toolkit will make use of and acknowledge existing software such as Primer3 where possible, and will contribute back in return to these projects, but will start afresh with the aim of allowing extensibility, modularity and the design of workflows that are currently impossible. At Aberystwyth we have a particular need for such a flexible toolkit, and will demonstrate its success on a complex case study of high-throughput primer design for seamless gene deletion.
Organisations
Publications
Aubrey W
(2015)
A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation.
in PloS one
Riley MC
(2013)
PD5: a general purpose library for primer design software.
in PloS one
Description | We have created a software library for the design of complex primers, which are short pieces of DNA used to prime an amplification reaction. We have used this to demonstrate a method for the deletion of genomic regions from multiple genomes. |
Exploitation Route | Commercial and forensic laboratories are all able to use this software library for primer design. Primer design is a necessity of most molecular biology laboratories. DNA amplification is used for identification (of species, or individual), for construction of new sequences (synthetic biology) and for other genetic manipulation techniques. |
Sectors | Digital/Communication/Information Technologies (including Software) Pharmaceuticals and Medical Biotechnology |
URL | http://www.aber.ac.uk/en/cs/research/cb/projects/pcr-primer-design/ |
Title | Precise Deletion Primers |
Description | This is a database of primer pairs for the precise deletion of genes from S. cerevisiae, S. pombe and L. lactis. |
Type Of Material | Database/Collection of data |
Year Produced | 2012 |
Provided To Others? | Yes |
Impact | We are still in the process of publishing. |
URL | http://precise-deletion.dcs.aber.ac.uk/ |
Title | PD5 |
Description | Software library for primer design.PD5 is a C++ software library of classes for the design and analysis of primers suitable for a wide range of PCR applications. It is open source and is currently being developed by the Bioinformatics group at the Institute of Maths, Physics and Computer Science, Aberystwyth University. http://code.google.com/p/primer-design/ |
Type Of Technology | Software |
Year Produced | 2013 |
Impact | No actual Impacts realised to date |
URL | http://code.google.com/p/primer-design/ |