How To Convert Db Format From Nih Blast To Blat Requirement

Question

[Sequer]

Hi I want to run a local BLAT for a huge set of short reads and intend to use BLAT for that. I find that the env_nt db from NCBI is in a different format whereas BLAT requires .fa, .nib or .2bit files to align against.

May I know how to convert the database to BLAT's needs?

Answer 1

[Neilfws]

If you already have env_nt in BLAST database format, you can dump the contents to a fasta file. This requires the command blastdbcmd (for the newer BLAST+) or fastacmd (for the older BLAST). See the BLAST Command Line Applications User Manual for details, or try fastacmd - or blastdbcmd -help at the command line.

Otherwise, just download env_nt in fasta format from the NCBI FTP site:

wget ftp://ftp.ncbi.nih.gov/blast/db/FASTA/env_nt.gz
gunzip env_nt.gz

[Sequer]

damn didn't know they had the FASTA format db. Thanks for your help.

[debocolman]

Hi, I want to convert 16S Microbial database (format LASst) in FASTA format? I know that I must use blastdbcmd commandline, but I can´t install BLAST programm. I want to use window version. Can you help me???

Thanks a lot!!!