Question: Blast+
0
gravatar for debocolman
7.9 years ago by
debocolman0
Argentina
debocolman0 wrote:

Hi, I would want to know if Blast+ program (Windows version) converts Blast database format in FASTA format? Is the blastdbcmd executable right to do it? And how I must write the orden for do it? I want to convert 16S Microbial database.

PLEASE HELP Me!!!!

Thanks!!!

blast+ • 2.1k views
ADD COMMENTlink modified 7.9 years ago by qiyunzhu430 • written 7.9 years ago by debocolman0
2

PLEASE DON'T SHOUT !!!!

ADD REPLYlink written 7.9 years ago by Pierre Lindenbaum131k

shhhhhhhhhhh...

ADD REPLYlink written 7.9 years ago by debocolman0
9
gravatar for a.zielezinski
7.9 years ago by
a.zielezinski9.2k
a.zielezinski9.2k wrote:

In Linux you can retrieve all fasta sequences from a blast database by typing:

blastdbcmd -entry all -db [blast_database] -out [blast_database].fasta

ADD COMMENTlink modified 7.9 years ago • written 7.9 years ago by a.zielezinski9.2k

Hi, this command does work,thx.

ADD REPLYlink written 4.2 years ago by 11255702470
0
gravatar for qiyunzhu
7.9 years ago by
qiyunzhu430
Buffalo
qiyunzhu430 wrote:

The latest version (2.27) use this command:

makeblastdb -in your16S.fasta -dbtype nucl -out db16S

I hope it's clear to you. Please let me know if you need further explanation.

Meanwhile, I think the 16S database is already there from the NCBI ftp. Did you check it out?

ADD COMMENTlink written 7.9 years ago by qiyunzhu430

Hi, the 16SMicrobial is a pre-formatted database. I just want to convert this database in FASTA format (because it isn´t in FASTA format). I´ve installed blast+ in Windows system but I´ve not could execute the command yet. I´ve read that blastdbcmd is the right correct. I´ve probed with your command but the error message says that File 16SMicrobial.fasta is empty (I don´t have any file .fasta because this is that I want it). I hope you understand me.

ADD REPLYlink written 7.9 years ago by debocolman0

Hi, sorry but I guess I miss understood your question... The command I posted actually converts FASTA into database, rather than the reverse... Sorry...

ADD REPLYlink written 7.9 years ago by qiyunzhu430

Hi, I really appreciate your response. Finally I could convert the 16S Microbial database in Fasta format. I realized that the blast+ folder was in the wrong place. Also, the blastdbcmd command was right. Thanks for all!!

ADD REPLYlink written 7.9 years ago by debocolman0
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