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

Question

[PeterC_NCBI]

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!

[frasercombe86]

When will this core_nt database be available for download

[GenoMax]

It is available for download now: https://ftp.ncbi.nih.gov/blast/db/

[rDNA]

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.

[GenoMax]

Yes it contains bacterial sequences

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