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I am helping a colleague setup a local blast server. My background is computer science so I apologize if I use incorrect terminology.

Using the NCBI blastn webpage, one of the databases listed is "NCBI Genomes (chromosome)." I'm unable to find this database listed on the database download page (ftp://ftp.ncbi.nlm.nih.gov/blast/db/).

What is the name of this database as listed on the ftp site?

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  • $\begingroup$ Have you tried contacting NCBI help? $\endgroup$ – James Oct 3 '17 at 3:41
  • $\begingroup$ In addition to NCBI, you can also use genomes from UCSC and Ensembl. $\endgroup$ – arhelion Oct 15 '17 at 3:07
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With the blast binaries you get a perl script update_blastdb.pl which you can use to download preformatted databases from the ncbi (it's pretty much a script that fetches the data from the location you found, anyway). With update_blastdb.pl --showall will list all available blast databases and probably refseq_genomic is what you need, unless your query is human data only.

However, that's based on the assumption that your query data is nucleotide data - you might need to choose different databases and tools for proteins

Unlike Maxim Kuleshov claims, the NC and NT accession prefixes don't differentiate between organisms, but genome assembly status, as stated in the linked documentation and the refseq release notes, section 3.8

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human_genomic.*tar.gz is Human RefSeq (NC_######) chromosome records with gap adjusted concatenated NT_ contigs and other_genomic.*tar.gz for non-human organisms (more about RefSeq accession numbers such as NC_ and NT_). You can find more information in the readme file.

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