In silico PCR - multiple Primers and multiple sequences at the same time
Hi all!
As a very new person in the world of bioinformatics. I would like to check primers I have designed agains multiple sequences. I have around 1000 primers and FASTA file with multiple sequences which is 20 GB. DO you recommend any particular tool.
Looking for some hints how to approach this challenge
Best :)
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sulichkarolina •
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Make a reference blast database of the 20GB fasta file and blast the primer sequences that you have. This will return 'hits' of single primers, but you should be able to identify the primer pairs that will give viable products based on their distances. You can subsequently refine the hits based on annealing temps (you'd need to calculate) and 5' alignment scores, etc....
How you suggest to do that on HPC?
I understand you have a steep learning curve...you should learn how to use blast from a command line.
What do you mean by "checking". Please add a representative output example.