Blast RNA nucleotide sequences with Protein-RNA complexes
Hi,
I have two datasets - one folder containing nucleotide sequences of different only RNA proteins and the other folder containing different protein-RNA complexes (all FASTA files). I want to blast each of the files in the first folder to find the most similar or close RNA sequences within the protein-RNA complexes (contained in the other folder).
How shall I do it?
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I don't understand what is a problem, just specify
-subject -queryand blast them.Do I need to do blastp or blastn? Also, I don't know much about blasting so if you could give an example it would be very nice.