Finding RNA sequence profile for a set of proteins
Hello everyone,
I have translated cds dateset and genomic RNA dateset for an organism. So it means I have Amino acid fasta file and nucleotide fasta file for one organism, which I have downloaded from NCBI genome organism browser.
Now for some specific protein I want to check which RNA sequences are associated for that gene/protein.
What is the right way to do it?
I have locus tag IDs and WP Ids(ProteinIDs) for the set of proteins.
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What do you mean by "check which RNA sequences are associated for that gene/protein"? You want to predict possible RNA-protein interactions between those sets or you want to find out which CDS may be translated from which RNA (the "genomic RNA dataset")?
From what I understand, the two datasets are for the same organism...?