How To Generate A Species Distribution From Blast Xml Output
4
0
Entering edit mode
10.8 years ago
whatup ▴ 30

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,

blast xml biopython python • 4.3k views
ADD COMMENT
1
Entering edit mode
ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
10.8 years ago
Peter 6.0k

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 COMMENT
1
Entering edit mode
10.2 years ago
Prakki Rama ★ 2.7k

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

ADD COMMENT
0
Entering edit mode
10.2 years ago
rob234king ▴ 610
Import into blast2go. Click statistics and species distribution. Should be that simple without python.
ADD COMMENT
0
Entering edit mode
10.2 years ago
Haluk ▴ 190

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 COMMENT

Login before adding your answer.

Traffic: 1026 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6