Description of nt database from NCBI
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3.3 years ago

Good afternoon,  I can't find how NCBI builds nt database, and what's the meaning of each file extension.  Can someone tell where I can read, how NCBI built NT database? I'm sorry for the random question.

database ncbi • 1.1k views
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3.3 years ago
GenoMax 141k

Likely using makeblastdb program included in blast+ just like we would do for a custom nucleotide database. You can actually get the fasta format file for nt here. Assuming you have enough RAM available (> 50G may be needed) you can build nt database yourself.

File types produced by formatdb were and likely are similar for makeblastdb.

nhr          deflines       binary    

nin          indices        binary       

nsq        sequence data    binary        


Nucleotide database formatted with "-o T" add these ISAM files:    

nsd          non-GI data    binary        

nsi         non-GI indices  binary
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