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Remove duplicates in two databases

Hello. I have two databases (.fas) that I have to unify in only one. Some sequences are present in both DB, I want to keep one copy and delete the other. Instead of removing manually one by one, is there any way to select all duplicates and remove them? Thank you very much.

sequences assembly database
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updated by GenoMax GenoMax • written by boudica5 • boudica5

'.fas' = fasta file ? (= just a file, not a database)

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

Dedupe.sh from BBMap should be able to do this. It will accept fasta files. Input is expected to be DNA.

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written by GenoMax GenoMax

Thank you, do you know if it accepts fasta files with protein sequences?

Also, citing Brian Bushnell from the link you gave me "However, I do have another program, filterbyname.sh, that can remove all sequences from a file that either share or don't share names with sequences in another file", again do you know if it accepts protein sequences?

My best regards

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written by boudica5 • boudica5

In that case you will need to use one of the solutions indicated by Pierre (though most of those appear to be for DNA too). BBMap tools are for DNA sequences AFAIK. I have edited my original post.

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written by GenoMax GenoMax

Dedupe strictly works on DNA (or RNA) sequences. However, filterbyname.sh should work on protein sequences if you use the aminoin flag... I've just never tested it. Note that, of course, it will only address the situations where sequence share identical or similar names (depending on the mode); it ignores the sequence itself.

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updated by Ram Ram • written by Brian Bushnell Brian Bushnell

I´ll try it! Thank you all for your kind responses

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written by boudica5 • boudica5

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