Question: Removing duplicate protein sequences from fasta file
1
gravatar for saadleeshehreen
15 months ago by
saadleeshehreen70 wrote:

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 • 595 views
ADD COMMENTlink modified 15 months ago by finswimmer13k • written 15 months ago by saadleeshehreen70
3
gravatar for finswimmer
15 months ago by
finswimmer13k
Germany
finswimmer13k wrote:

Use seqkit:

$ seqkit rmdup input.fa > output.fa
ADD COMMENTlink modified 15 months ago • written 15 months ago by finswimmer13k

Thanks a lot! It works.

ADD REPLYlink written 15 months ago by saadleeshehreen70

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

ADD REPLYlink written 15 months ago by Emily_Ensembl20k

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

ADD REPLYlink modified 15 months ago • written 15 months ago by RamRS25k
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