Getting Taxonomy Lineage From Ncbi Gi Or Accession Number

Question

[Abhi]

Hey Guys

I have a specific question about getting a taxonomic lineage, given a NCBI accession or GI number. I have in the past used the module from CPAN (below) but I belv it only works for GI's and not NCBI Accession. Efecthing using NCBI etuils is not an option as we need to make millions of queries/weeks for blast results.

Bio::LITE::Taxonomy::NCBI link

Just wondering if there are other ways to this with no dependency on fetching stuff from internet.

[Pierre Lindenbaum]

exact duplicate of http://www.biostars.org/post/show/10959

[Abhi]

@Pierre : with due respect the two posts are not exactly same. I was looking for NCBI GI to taxonomy lineage i.e Superkingdom:Kingdon:Phylum:Class etc and not necessarily just NCBI tax id.

Answer 1

[Neilfws]

For "millions of queries", you will want a local copy of the taxonomy database.

Start with the FTP site and consult the readme files to see which is appropriate for you. One option is to load the taxonomy into a BioSQL instance as described here.

[Abhi]

I guess thats what I will eventually do....I was just wondering if someone has already built something similar that I could use.

[deepthithomaskannan]

Try this link Parsing NCBI taxonomic tree?

Answer 2

[-_-]

First, you need to map accession numbers (GI is deprecated) to tax ids based on *accession2taxid.gz files from here, ftp://ftp.ncbi.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz. Then based on a tax id, you can trace its whole lineage.

The whole NCBI taxonomy database is not that big. I have written some code to convert NCBI taxdump into lineages identified by tax ids, https://github.com/zyxue/ncbitax2lin. You may find it useful.