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News: New more compact NCBI BLAST Core Nucleotide Database (core_nt) now available on the web

NCBI now offers the core nucleotide database (core_nt), an alternative to the default nt database that contains better-defined content and is less than half the size of nt.

Benefits of BLAST core_nt over nt

  • Enables faster searches
  • Returns similar top results for most searches
  • Reduces redundancy for some highly represented organisms
  • Allows easier download and requires less storage space for database download for standalone BLAST (downloads available in August)

Note: core_nt will become the default nucleotide database in August 2024.

See our NCBI Insights post for more details and Try it out!

ncbi blast
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updated by GenoMax GenoMax • written by PeterC_NCBI • PeterC_NCBI

When will this core_nt database be available for download

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written by frasercombe86 • frasercombe86

PeterC_NCBI the core_nt also contains bacterial sequences, right? The NCBI post states "Core_nt contains the same eukaryotic transcript and gene-related sequences as nt. The core_nt database is nt without most eukaryotic chromosome sequences. " and thereby only mentions eukaryotes.

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written by rDNA • rDNA

Yes it contains bacterial sequences

$ blastdbcmd -db core_nt -taxids 2 -outfmt %S 
Arthrobacter sp.
Vibrio parahaemolyticus
uncultured Chloroflexota bacterium
Bacillus aerophilus
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written by GenoMax GenoMax

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