Question: Remove duplicate protein sequences having different fasta identifiers
0
gravatar for utkarsh.sood
2.7 years ago by
utkarsh.sood30
India
utkarsh.sood30 wrote:

Hello

I have 9058 faa files. some are having duplicate protein sequences but with unique different fasta identifiers. How these duplicate sequences can be removed?

Thanks!

alignment sequence • 1.7k views
ADD COMMENTlink modified 2.7 years ago by Sej Modha4.0k • written 2.7 years ago by utkarsh.sood30
1

The answer below is fantastic. I'd point out that strictly speaking these aren't necessarily duplicate sequences. They could be if someone just made a mistake with FASTA headers, but chances are they are protein sequences of the same protein from different organisms, or strains, or isolates, etc. They may be identical sequences, and you may only want a single representative in those cases, in which case Sej's answer below with clustering will solve it. But for clarity, Identical sequences doesn't necessarily equate to duplicate sequence.

ADD REPLYlink written 2.7 years ago by Dan Gaston7.1k
4
gravatar for Sej Modha
2.7 years ago by
Sej Modha4.0k
Glasgow, UK
Sej Modha4.0k wrote:

You can use cd-hit with 1.0 identity and redundancy 1 (-t parameter) to do this.

ADD COMMENTlink written 2.7 years ago by Sej Modha4.0k

yep cluster the sequences. One representative will be kept.

ADD REPLYlink written 2.7 years ago by ALchEmiXt1.9k
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