How To Generate A Species Distribution From Blast Xml Output

Question

[whatup]

Hi,

I am very new in bioinformatics field. I have a BLAST XML output file and I need to parse it to generate a species distribution. I was hoping someone could show me how it can be done by Biopython with some examples.

thank you,

[Pierre Lindenbaum]

see also

Taxonomy of blast hits

[Pierre Lindenbaum]

I don't remember: does the taxon-id appear in some BLAST-XML output ? show us a snippet of XML please.

Answer 1

[Peter]

Sadly the BLAST XML does not (yet) include the taxonomy id as a nice field. Depending on the database used, you may get the species names in the hit descriptions. Other than that, you would need to separately map from the hit gene/protein ID to its species.

If you use the BLAST tabular output, you can get the species, kingdom, taxid, etc as dedicated columns (new in BLAST+ 2.2.28, see http://blastedbio.blogspot.co.uk/2012/05/blast-tabular-missing-descriptions.html for background). This would probably be easiest.

See also: Blobology aka assemblage from the Blaxter Lab in Edinburgh, http://www.nematodes.org/bioinformatics/blobology/index.shtml and https://github.com/blaxterlab/blobology

Answer 2

[Prakki Rama]

This is not biopython, but you can simply load XML file in Blast2go tool and generate species distribution.

Answer 3

[rob234king]

Import into blast2go. Click statistics and species distribution. Should be that simple without python.

Answer 4

[Haluk]

You can perform the taxonomy assignment, including BLAST, in Qiime. It gives you an OTU table. Then you can even get the taxonomy plots in different form of plots.