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Blast+

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+
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updated by qiyunzhu qiyunzhu • written by debocolman • debocolman

3 answers

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

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

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written by Andrzej Zielezinski Andrzej Zielezinski

Thank you for all a.zielezinski!!!

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written by debocolman • debocolman

FYI: Put this as a comment!!! NOT as an answer

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written by Rm Rm

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?

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written by qiyunzhu qiyunzhu

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.

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written by debocolman • debocolman

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

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written by qiyunzhu qiyunzhu

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!!

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written by debocolman • debocolman

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