Question: Classification of bacteria - bioinformatics
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gravatar for Mohak
11 days ago by
Mohak0
Mohak0 wrote:

I want to do an enrichment analysis across all bacterial phyla/classes. For this I first need to know, of all the genomes I have in my database, how many of them are gammaproteobacteria, spirochetes etc. A list which gives the names of these bacteria, their type and their accession number. Is there a repository which can give me this information?

ADD COMMENTlink modified 11 days ago by Lina F50 • written 11 days ago by Mohak0
0
gravatar for Lina F
11 days ago by
Lina F50
Boston, MA
Lina F50 wrote:

I don't know if there is an easy ready-made answer for this question, but KEGG has a rudimentary "tree" of sorts:

http://www.genome.jp/kegg/catalog/org_list.html

You could download this html file and parse it and it will give you the links to genbank. Maybe Python's beautifulsoup module can help there.

If you know your way around NCBI, you could use the eUtils API to access different databases (i.e. the Taxonomy database to get the phylogenetic lineages).

Here are some notes on how to use eUtils with Python: http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc110

Both of these solutions will probably need a bit of finagling and are not super elegant. Maybe someone else has a more sophisticated solution :-)

ADD COMMENTlink written 11 days ago by Lina F50

Thanks Lina! I wasn't aware of the KEGG tree. Beautifulsoup solves the problem!

And never used the eUtils API, but the biopython link seems useful. Will definitely try that out. Thanks a ton! :)

ADD REPLYlink written 11 days ago by Mohak0
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