I generated a series of local BLAST databases using makeblastdb of metagenomic data and am searching for the presence of a particular gene. While I can do the normal BLAST analysis looking at e-values, % identity, etc. I haven't been able to figure out how to determine how many times a given sequence exists in the database.
So: given a BLAST database of metagenomic data where a particular gene may exist multiple times, how do I determine the copy number of a given BLAST hit?
Thanks in advance.
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