Software Auto Corrects Disease-Causing Genes
July 8, 2015| |
Alison Testa, a PhD student from Curtin University's Centre for Crop and Disease Management (CCDM) in Western Australia has created CodingQuarry, a gene-prediction software that allows finding fungal genes a lot quicker and more reliable. Miss Testa said that CCDM is interested in finding important genes in fungi that allow fungal pathogens to infect their crops. CodingQuarry uses two techniques, hidden-Markov-model prediction and alignment of RNA-seq transcriptome sequences.
One disease the team has been working on is the Pyrenophora Net Blotch, an important barley disease caused by the pathogen Pyrenophora teres f. teres. Using CodingQuarry, they found 1,000 new genes and made corrections to a few thousands of the known 13,000 genes in Pyrenophora Net Blotch. "In terms of time saved, if you were going to manually correct genes based with RNA-seq, it takes months and months and is very labor intensive, whereas using CodingQuarry, the same outcome can be achieved in about 10 minutes," said Miss Testa.
For more information, read the news release at the Science Network Western Australia website.
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