Ncbi Wgs/Nt/Env-Nt Databases

Question

[Lythimus]

I am currently BLASTning against NCBI's NT database but I am considering also using WGS and ENV-NT. I was given the impression that WGS was populated by pulling from ENV-NT if the sequence was definitively classified to a specfific organism but after looking at the file sizes it seems the reverse. Could someone explain to me clearly the differences in NT, ENV-NT and WGS and maybe give an example of when I would and possibly wouldn't want to use specific databases or sets of databases?

Just assume whatever domain you are most familiar with and use those in your examples please.

Answer 1

[Alex]

Useful page with NCBI databases description

nt contains all GenBank + RefSeq Nucleotides + EMBL + DDBJ + PDB sequences (excluding HTGS0,1,2, EST, GSS, STS, PAT, WGS). No longer "non-redundant".

wgs is collection of partially assembled sequences from the genome centers. These are contigs assembled directly from whole genome shotgun sequencing.

env_nt contains DNA sequenced directly from the environment (from all organisms mixed together, e.g. Sargasso Sea and Mine Drainage projects)

Additionaly check:

est contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags". More here http://www.ncbi.nlm.nih.gov/pubmed/8401577?dopt=Abstract

htgs - unfinished High Throughput Genomic Sequences: phases 0, 1 and 2 (finished, phase 3 HTG sequences are in nr). About phases here.

gss - Genome Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences. More here.

sts - contains sequence data for short genomic landmark sequences or Sequence Tagged Sites. More here

[Alex]

All WGS sequences - yes (genome project), ENV_NT sequeneces - usually not.

[Lythimus]

This may be a silly question. Are sequences from WGS and ENV_NT taxonomically classified (as in NT) and aren't solely associated with the environment from which they were harvested?