I want to convert 16S Microbial pre-formatted database 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.
Your question is difficult to fully understand. Presumably, you are using SILVA, RDP classifier, GreenGenes, or another 16S sequence database for meta-taxonomic sorting of bacterial/archaea rRNA sequences derived from environmental samples.
It's hard to determine what exactly your problem is. Perhaps you had an error in the untar/unzip of your database and are missing a file or part of a file? It's hard to tell.
In any event, the following statement: "The problems are that I don´t know how I have to write right the commannd" has me thinking that you really need to start at reading the documentation to understand what you are doing. The BLAST wiki is a good place to start and NCBI has a great list of executables at their FTP. This is also a good reference for you and you can't go wrong by reading this book.
You will want to first make sure the database you downloaded isn't corrupted. Assuming everything is fine with the database (named "my_db" below) you can dump a fasta with:
blastdbcmd -db my_db -entry all > my.fasta
Where "my.fasta" will be the file with your sequences.
See also this pervious question from yesterday: Blast+