Aassign taxonomy for oomycetes

[Alberto Rojas]

Hi every one,

I'm working currently about soil oomycete microbial diversity. And my question is, which database I should be to use for assign taxonomy into these microorganisms. I downloaded the Levesque and Robideau sequences, but I don't sure if I should be to use it!

Thanks in advance for your help!

Cheers!!!

[Colin Brislawn]

Good morning Alberto,

I would start with the default database (greengenes) and see how well that works.

Formatting databases is tricky, let's see how well greengenes works before starting the process of building a new one.

Colin

[Chris Baker]

What marker gene are you using, Alberto? Levesque and Robideau use COI, don't they? Colin, I thought greengenes was just 16S, no?

Cheers,

Chris

[Colin Brislawn]

Oh, oomycete are part of Eukaryota. Whoops!

Yes, the greengenes will not work well for those. Chris is asking the right question; which gene was amplified?

If the 18S gene was amplified, using the 18S part of SILVA might work well. If the ITS gene was used, UNITE is a pretty good database. Qiime compatible version of both databases are listed on this page: 

http://qiime.org/home_static/dataFiles.html 

If a specific gene was used, say COI, you will need to find a matching database. Hopefully someone has already made a qiime compatible version of this database.

Any advice here, Chris? I've mostly worked with common marker genes.

Colin