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I want to convert 16S Microbial database format in fasta format. I use Blast+ program (2.2.27+ version Window). I could install this program and I know that I must to use blastdbcmd command. The problems are that I don´t know how I have to write right the commannd and also, I have an error message: No alias or index file found nucleotide database 16SMicrobial in search path C:users\Debora\blast-2.2.27+; C:users\Debora\blast-2.2.27+\db\16SMicrobial

The 16S Microbial file is in db file. The 16S Microbial is ungzipped and untarzipped.

I tried to edit the environment variable, I intented to edit the User and System variable but I don´t really understand what I must write. So, I suspect that the database is in the wrong place, but I don´t know how to correct.

I´ll hope someone can help me!!!!!

Thanks for all!!!

user1892205
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What's happening is your blastdbcmd program cannot find your 16s database. You need to have the database set up as .phr/.pin/.psq or .nhr/.nin/.nsq files first. Then you have to make sure your program knows where to look. The easiest way is to use a .ncbirc file, and this file should be in the same directory as your actual blastdbcmd executable. On Windows the file would be .ncbi.ini I think, but I'm not sure. I also don't know the format, but you should be able to google that. To give you an idea on my mac the file contains the line BLASTDB=/Users/myName/blast/db, where that directory is where I'm storing my databases.

DaveTheScientist
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