At NSW DPIRD I’m building, from scratch, software that designs and checks DNA-based diagnostic tests for plant pathogens. Fast, reliable tests are a first line of defence in biosecurity, but designing a good one by hand is slow and easy to get wrong. This pipeline automates the whole job, from raw sequences to a ranked shortlist of tests.
- Collect. Downloads and prepares the genome sequences for any organism you choose.
- Find targets. Locates the DNA regions that tell the target apart from its close relatives.
- Design. Generates every feasible test in those regions, aiming to catch as many known variants of the pathogen as possible. It covers PCR, qPCR, LAMP and CRISPR-based tests, plus multiplex tests that look for several targets at once and degenerate primers that tolerate natural variation in the DNA.
- Check quality. Screens every design for the things that make tests fail in the lab: primers that fold back on themselves or stick to each other, runs of repeated bases, and poorly matched melting temperatures.
- Report. Returns the best candidates, with statistics on how many variants of the species each one detects.
Already have primers? A second mode takes them as input, reports how well they perform and how many variants they capture, and suggests better primers aimed at the same region.
A graphical interface lets non-specialists run it without any bioinformatics, while adjustable thresholds and settings give experienced users full control.
- Status
- In development
- Built by
- NSW DPIRD, in collaboration with Deakin University
- Funding
- Australian Government Department of Agriculture, Fisheries and Forestry (DAFF)
- Validation
- Deakin University is testing the pipeline on three different pathogen systems