Hello all, I am new here and new to QIIME 2. My -omics knowledge is very rusty and out-of-date but I have been getting back on the horse with the excellently written tutorials.
My new project will involve taking 16S rRNA-Seq data and designing CLASI-FISH probes against the species found within the population, which will then be applied to confocal microscopy. Probes need to have high affinity for their target species and minimal affinity for non-target species.
The process of probe design would probably involve making a multiple alignment of all the 16S sequences, going through each target species/OTU iteratively to find regions of n bases that are dissimilar to the other species/OTU, and blasting these against database whole genome sequences to score their likelihood for off-target binding.
I have three questions at this stage:
- Is there already a plugin that has this feature, or a way to replicate this functionality with a bit of a hack?
- Is it silly to consider doing this within QIIME 2, and if so should I just be exporting to elsewhere
- If there’s no way to do it, but it seems like a worthwhile module to make, will this be a particularly difficult workflow for me (a fairly experienced programmer) to craft into a new module?