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What'S The Different Between Formatdb (In The Legacy Blast) And Makeblastdb (In Blast+)?

Hi all, in the legacy BLAST, the command formatdb is used for formating fasta files into BLAST database. Then in BLAST+, makeblastdb is used. And I tried to apply blastx+ on a database formatted by formatdb, it doesn't give me errors but would the result be wrong?

What is the difference between formatdb and makeblastdb? Do they give the same result? As I had a couple of data ran (used blastx+) on a database which was formatted by using formatdb. Do I need to re-run them? Thanks in advance.

blast blast makeblastdb
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updated by Brandon Wilson • Brandon Wilson • written by Ken Ken

2 answers

NCBI just renamed their formatdb executable (in the C branch) to makeblastdb (C++ branch). They both produce the same database (when using the same version), so no need to rerun anything.

What might happen is that the database format is changed a little between versions, but then BLAST won't run at all (i.e., give an error).

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written by Michael Schubert Michael Schubert

thanks michael.

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written by Ken Ken

Is there a way to use makeblastdb, or any other utility, to update the version of a blast db that was created using formatdb? It looks like BLAST+ only wants to run with version 4 DB's. Thanks!

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written by Brandon Wilson • Brandon Wilson

Hi Brandon, welcome to BioStar. Please delete this comment and ask this as a new question.

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written by Casey Bergman Casey Bergman

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