Which BLAST output format can give full taxonomony information

[SDPA_Pet]

Hi, I was wondering which BLAST output format I should use to do this. I want to blast against nt database. I want the output not only gives me genus and species name, but also gives me phylum, order, family name.

Is it possible?

[jameslz]

you can use the GI number to map the tax id and the get the complete taxonomic lineage information via taxdump.tar.Z. ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/

[SDPA_Pet]

Is it possible to map it when I blast it? or I need to get blast result first and then map to tax?

Which command I should use to map the tax id?

[jameslz]

blast output format 6, 7, and 10 can be additionally configured to produce a custom format , it includes the Subject Taxonomy ID (staxids flag),
for example:

blastx -query Human_kinase_rna-100.fasta -db ../ccds/CCDS_protein.20130430 -out Human_kinase-rna-blastx-m7.tbl -evalue 1 -outfmt “7 qseqid qlen slen qcovhsp sseqid staxids bitscore score evalue pident qstart qend sstart send” -num_alignments 10 -num_threads 8

I use a perl script to fetch the complete taxonomic lineage information of the blast staxids.

[SDPA_Pet]

blast output format 6, 7, and 10 can be additionally configured to produce a custom format , it includes the Subject Taxonomy ID (staxids flag),
for example:

I use a perl script to fetch the complete taxonomic lineage information of the blast staxids.

Do I need to put the complete taxonomic lineage information file (ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/) in the same folder with my database file? In your example, I didn't see your command call any taxonomic lineage information file.

[SDPA_Pet]

Hi use format 7 and use your command settings

I still do have the taxonomic lineage and I don't know how to use the taxonomic lineage file

Here is my output.

query id query length subject length % hsp coverage subject id subject tax ids bit score score evalue % identity q. start q. end s. start " s. end "
denovo0 266 297 85 gi|14718977|gb|AF352544.1| 163259 351 190 1.00E-93 95.15 39 265 1 219
denovo1 400 1178 100 gi|117572484|gb|DQ979290.1| 1211 706 382 0 98.5 1 400 670 1069

[jameslz]

Usage:

perl tax_trace.pl nodes.dmp names.dmp taxids.txt taxids_export.txt

input file:taxids.txt
format: seqId taxId

gl00001 192
gl00002 2020

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


output file:taxids_export.txt

gl00001 Azospirillum brasilense root|cellular organisms|Bacteria|Proteobacteria|Alphaproteobacteria|Rhodospirillales|Rhodospirillaceae|Azospirillum|Azospirillum brasilense no rank|no rank|superkingdom|phylum|class|order|family|genus|species
gl00002 Thermomonospora curvata root|cellular organisms|Bacteria|Actinobacteria|Actinobacteria|Actinobacteridae|Actinomycetales|Streptosporangineae|Thermomonosporaceae|Thermomonospora|Thermomonospora curvata no rank|no rank|superkingdom|phylum|class|subclass|order|suborder|family|genus|species

[SDPA_Pet]

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

Thank you. Can you also post your "taxids.txt" and "taxids_export.txt" file. I need to make sure my input file format is right and the output file is what I want. The attachment is my blastoutput and taxid. It didn't work.
Thank you.

[jameslz]

You can parse the blast out file using:

cut -f1,6 blastout.txt >taxids.txt

and then:

perl tax_trace.pl nodes.dmp names.dmp taxids.txt taxids_export.txt

[SDPA_Pet]

Hi, what does this mean? "cut -f1,6 blastout.txt >taxids.txt"

[jameslz]

Hi, what does this mean? "cut -f1,6 blastout.txt >taxids.txt"

Linux Command, Get the first and the sixth collumn (taxids)

[SDPA_Pet]

Oh, my taxon id is the 5th column. I have another attachment in my post. Is that correct? I can't get taxon information from that file.

[jameslz]

Just fetch the "query id" and "tax ids" collumn .

[maubp]

Which BLAST output format can give full taxonomony information?

Not the XML output (for now), but the optional taxonomy columns in the tabular/comma separated output get you close:

http://blastedbio.blogspot.com/2014/02/blast-xml-output-needs-more-love-from.html

[yzzhang]

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