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

Question

[Ken]

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.

Answer 1

[Michael Schubert]

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).

[Ken]

thanks michael.

Answer 2

[Brandon Wilson]

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!

[Casey Bergman]

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