Question: How To Generate A Species Distribution From Blast Xml Output
0
gravatar for whatup
7.1 years ago by
whatup30
United States
whatup30 wrote:

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,

xml biopython blast python • 3.2k views
ADD COMMENTlink modified 6.5 years ago by Haluk190 • written 7.1 years ago by whatup30
1

see also

Taxonomy of blast hits

ADD REPLYlink written 7.1 years ago by Pierre Lindenbaum134k

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

ADD REPLYlink written 7.1 years ago by Pierre Lindenbaum134k
1
gravatar for Peter
7.1 years ago by
Peter5.9k
Scotland, UK
Peter5.9k wrote:

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

ADD COMMENTlink written 7.1 years ago by Peter5.9k
1
gravatar for Prakki Rama
6.5 years ago by
Prakki Rama2.4k
Singapore
Prakki Rama2.4k wrote:

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

ADD COMMENTlink written 6.5 years ago by Prakki Rama2.4k
0
gravatar for rob234king
6.5 years ago by
rob234king600
UK/Harpenden/Rothamsted Research
rob234king600 wrote:
Import into blast2go. Click statistics and species distribution. Should be that simple without python.
ADD COMMENTlink written 6.5 years ago by rob234king600
0
gravatar for Haluk
6.5 years ago by
Haluk190
Lincoln, Nebraska
Haluk190 wrote:

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.

ADD COMMENTlink written 6.5 years ago by Haluk190
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