What is in the NCBI chromosome nucleotide database vs nt/refseq_genomic?

Question

[lauraeiv]

What kind of sequences are in the NCBI chromosome database compared to nt or refseq? The definition on the blast page for the chromosome one is unclear to me.

Thanks

[5heikki]

Maybe it's only fully sequenced molecules? You could email them and ask..

Answer 1

[Siva]

The databases are described in this NCBI guide.

How to BLAST guide (Table 2)

Database    Type         Content
                         All GenBank + EMBL + DDBJ + PDB sequences,
nr (nt)     Nucleotide   excluding sequences from PAT, EST,
                         STS, GSS, WGS, TSA and phase 0,
                         1 or 2 HTGS sequences, mostly non‐redundant.

chromosome  Nucleotide   Complete genomes and complete chromosomes from the NCBI Reference Sequence project.

[5heikki]

Quite a fun place to hide such information. Too bad now they're exposed and the almighty Google will know.

[Siva]

ha. ha. I agree. Though, there seems to be a link to this file in the BLAST help page (Guide to BLAST home and search pages)

[lauraeiv]

Excellent thank you, very sneaky alright!