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grunwaldlab / effectR

An R package to call oomycete effectors
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Close this "Does not find CRN domains in P. infestans proteome" #26

Open eriklysoe opened 6 months ago

eriklysoe commented 6 months ago

Forget about it, I guess I need to find ORFs with EMBOSS, not gene predicted using augustus on a masked genome

Hi

I used your effectR for the first time, and it finds many RxLRs in around 20000 proteins. But when I shift to "CRN" motif it finds none, but I can find many LFLAK domains manually. Not shure what I'm doing wrong.

Cheers Erik

fasta.file = "/home/augustus.aa" ORF <- seqinr::read.fasta(fasta.file) length(ORF) [1] 20834 crn.cand <- regex.search(ORF,motif = "CRN") Error in regex.search(ORF, motif = "CRN") : No CRN sequences found.

From your publication "Changing the motif="RxLR" option to “CRN” or “custom” will allow the prediction of these other motifs of interest without reloading the ORF dataset, thus significantly reducing processing time."