Question: What'S The Different Between Formatdb (In The Legacy Blast) And Makeblastdb (In Blast+)?
gravatar for Ken
8.2 years ago by
Ken150 wrote:

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.

makeblastdb blast • 9.2k views
ADD COMMENTlink written 8.2 years ago by Ken150
gravatar for Michael Schubert
8.2 years ago by
Cambridge, UK
Michael Schubert6.9k wrote:

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).

ADD COMMENTlink written 8.2 years ago by Michael Schubert6.9k

thanks michael.

ADD REPLYlink written 8.2 years ago by Ken150
gravatar for Brandon Wilson
7.8 years ago by
Brandon Wilson0 wrote:

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!

ADD COMMENTlink written 7.8 years ago by Brandon Wilson0

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

ADD REPLYlink written 7.8 years ago by Casey Bergman18k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1210 users visited in the last hour