A Workflow-based High Throughput Toolkit for Primer Design

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.

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.