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Question: List record in a local BLAST database
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gravatar for songzewei
5.8 years ago by
songzewei • 10
United States
songzewei • 10 wrote:

Is there a way to get a FASTA file containing all the record in a local BLAST database.

I've created a local database using makeblastdb with a fasta file, but was wondering if there is any way to reverse this process?

 

Thanks!
blast sequence database fasta • 1.9k views
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modified 5.8 years ago • written 5.8 years ago by songzewei • 10
1
gravatar for songzewei
5.8 years ago by
songzewei • 10
United States
songzewei • 10 wrote:

I found the corresponding fastacmd in blast+, it is blastdbcmd.

blastdbcmd -db database -entry all -out database.fasta
ADD COMMENT • link written 5.8 years ago by songzewei • 10
0
gravatar for Felix Francis
5.8 years ago by
Felix Francis • 510
United States/University of Delaware
Felix Francis • 510 wrote:

Use "fastacmd" to generate a single fasta file from an existing BLAST database

You can use the following arguments along with it:

-d    BLAST database (the default is "nr")
-D    1 (dump the database in fasta format)
-o    filename for the output

Example: fastacmd -d cdna -D 1 -o seq.fasta

 
ADD COMMENT • link modified 5.8 years ago • written 5.8 years ago by Felix Francis • 510

fastacmd in not included in the latest blast+, is there a new command for this? I tried to search the blast+ document but cannot find it.

ADD REPLY • link written 5.8 years ago by songzewei • 10
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