Question: Classification of bacteria - bioinformatics
gravatar for Mohak
4 months ago by
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 4 months ago by Lina F80 • written 4 months ago by Mohak0
gravatar for Lina F
4 months ago by
Lina F80
Boston, MA
Lina F80 wrote:

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

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:

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 4 months ago by Lina F80

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 4 months ago by Mohak0
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