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I've written a little script to remove identical sequences from fasta to get what I need. To print the list of removed sequences, uncomment line 22 #! /usr/bin/python3 # Removes identical sequences from fasta file import sys from Bio import SeqIO sequences={} #This is where sequences will be stored #likely calling str(seq.seq) on every test will be slower ...


I'm not sure if there's a way on GenBank, but UniProt offers UniRef where you can cluster redundant sequences or specify a lower cutoff (like 90% identity).

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