Question: Mapping NCBI Genome Accessions - NCBI Taxonomy IDs
0
gravatar for mar.ark.parr
9 months ago by
mar.ark.parr40
mar.ark.parr40 wrote:

Hi all,

I have list of NCBI genome accessions (SAMN02441064, NC_014374, NZ_ACYB00000000 ...) and would like to know taxonomic IDs of the species that they belong to.

Is there a mapping file somewhere? Or how can I find their taxonomic IDs programmatically?

Thanks in advance, Marina

genbank taxonomy ncbi genome • 566 views
ADD COMMENTlink modified 9 months ago by genomax84k • written 9 months ago by mar.ark.parr40
1
gravatar for a.zielezinski
9 months ago by
a.zielezinski9.1k
a.zielezinski9.1k wrote:

The directory ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/ provides mapping files between the accession.version (from a nucleotide, protein, WGS or TSA sequence record) and a taxonomy ID.

ADD COMMENTlink written 9 months ago by a.zielezinski9.1k

Thanks a lot for the answer!

ADD REPLYlink written 9 months ago by mar.ark.parr40
1
gravatar for genomax
9 months ago by
genomax84k
United States
genomax84k wrote:

If these are all nucleotide accessions then you can also use NCBI EntrezDirect:

$ esearch -db nuccore -query "SAMN02441064" | elink -target taxonomy | esummary | xtract -pattern DocumentSummary -element TaxId
1052825
$ esearch -db nuccore -query "NC_014374" | elink -target taxonomy | esummary | xtract -pattern DocumentSummary -element TaxId
666510
ADD COMMENTlink written 9 months ago by genomax84k

Thank you for the answer!

ADD REPLYlink written 9 months ago by mar.ark.parr40
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