New more compact NCBI BLAST Core Nucleotide Database (core

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

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5 months ago

PeterC_NCBI ▴ 520

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 • 1.5k views

ADD COMMENT • link updated 4 weeks ago by GenoMax 148k • written 5 months ago by PeterC_NCBI ▴ 520

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When will this core_nt database be available for download

ADD REPLY • link 4 months ago by frasercombe86 • 0

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

ADD REPLY • link 4 months ago by GenoMax 148k

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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.

ADD REPLY • link 4 weeks ago by rDNA ▴ 20

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Yes it contains bacterial sequences

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

ADD REPLY • link 4 weeks ago by GenoMax 148k

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