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Removing duplicate protein sequences from fasta file

Hi, I want to do psiblast in command line. Before, performing psiblast, I tried to make a blast database by using makeblastdb command. But it shows the following error:

BLAST Database creation error: Error: Duplicate seq_ids are found:
REF|WP_003261842.1

My fasta file is very large. So, manual deletion of the duplicate sequence is nearly impossible. How can I get rid from the duplication?

Cheers

blast database makeblastdb
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updated by finswimmer finswimmer • written by saadleeshehreen saadleeshehreen

1 answer

Use seqkit:

$ seqkit rmdup input.fa > output.fa
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written by finswimmer finswimmer

Then please accept his answer. There's a little tick box.

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written by Emily Emily

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

Upvote|Bookmark|Accept

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written by Ram Ram

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