[maubp]

I think blast+ has option to include taxonomy information. the "sscinames" option --- unique Subject Scientific Name(s)

Yes, but only in the tabular or comma separated output:

• staxids means Subject Taxonomy ID(s), separated by a ';'
• sscinames means Subject Scientific Name(s), separated by a ';'
• scomnames means Subject Common Name(s), separated by a ';'
• sblastnames means Subject Blast Name(s), separated by a ';' (in alphabetical order)
• sskingdoms means Subject Super Kingdom(s), separated by a ';' (in alphabetical order)
• stitle means Subject Title
• salltitles means All Subject Title(s), separated by a '<>'

None of these give the full taxonomy lineage, which is what I think was being asked for here (see the earlier comments).

See also http://blastedbio.blogspot.co.uk/201...criptions.html

[lilicano]

thanks for your tax_trace.pl script solution!

Thanks so much jamslz, your script works great. I dont know but the sskingdoms option had never worked for me.

you made my day with this post!

Best,

Lili

Usage:


input file:taxids.txt
format: seqId taxId


nodes.dmp names.dmp can be download from taxdump.tar.Z (ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/)


output file:taxids_export.txt

[sme.bug]

Thanks for sharing! This was very helpful to me.

[maubp]

I believe the fairly new BLAST XML v2 output also includes taxonomy information, if available.

[Brian Bushnell]

Just thought I'd mention JGI's new Taxonomy server. You can look up organism names, gi numbers, or accession numbers to get either the NCBI taxid or complete lineage. These are all in the nt sequence headers.

[ellygoetz]

Hi,

I know I am entering this discussion many many years later but is the perl script still available? I am struggling to find a way to extract full taxonomic information using my blastn taxid outputs and this looks like a great lead!