Question: Mapping NCBI Genome Accessions - NCBI Taxonomy IDs
0
gravatar for mar.ark.parr
6 days ago by
mar.ark.parr30
mar.ark.parr30 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 • 90 views
ADD COMMENTlink modified 6 days ago by genomax70k • written 6 days ago by mar.ark.parr30
1
gravatar for a.zielezinski
6 days ago by
a.zielezinski8.7k
a.zielezinski8.7k 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 6 days ago by a.zielezinski8.7k

Thanks a lot for the answer!

ADD REPLYlink written 17 hours ago by mar.ark.parr30
1
gravatar for genomax
6 days ago by
genomax70k
United States
genomax70k 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 6 days ago by genomax70k

Thank you for the answer!

ADD REPLYlink written 17 hours ago by mar.ark.parr30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1105 users visited in the last hour