greengenes OTU Id

[JQL]

Hi

I think the OTU id we use in greengenes database is unique. Even the same species may have different OTU ids, suggesting they belong to different strains etc. 

How to find more information about this particular OTU id? 

1) search greengenes database using the taxonomy information, but this is not unique to this particular OTU id?

2) take the sequence from the id, and blast NCBI  database?

Just wondering. thanks,
John

[Daniel McDonald]

Hi John,

There is a unique Greengenes ID for every unique NCBI accession (incl. version) that is indexed by Greengenes. These IDs have nothing to do with taxonomy. Regarding your specific questions:

 

How to find more information about this particular OTU id? 

Second Genome has committed to redoing the old webservices but they are not online yet unfortunately. However, what I recommend in the mean time is to search for the IDs of interest in:

ftp://greengenes.microbio.me/greengenes_release/gg_13_5/gg_13_5_accessions.txt.gz

And then search NCBI with the accession to get complete details. Alternatively, you can grab the MySQL database and deploy it but that assumes you've got familiarity with MySQL.

Best,

Daniel

  

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[JQL]

thanks Daniel. That is very useful.

the link contains gg_13_5. Is gg_13_8 available by any chance?

thanks

John

[Daniel McDonald]

It's identical, the only change with 13_8 was an update to the taxonomy associated with the OTUs

-Daniel

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[JQL]

thanks. My MySQL is bit rusty after graduate school. What is the database? 

[JQL]

The genebank accession id is assigned by blasting the 16S sequence (corresponding to the OTU ID) to the genebank bacterial genomes?

[JQL]

Hi Daniel,

 

Sorry I have more questions. Since you mentioned the IDs have nothing to do with taxonomy. We find that there are several different OTU IDs that share the exactly same taxonomy, inlcluding at the species level. Do you suggest they are the same lineage and we combine them? Before we thought they were different lineages perhaps at strain level. What do you do with those OTU IDs with identical taxnomy? Please advise.

 

thanks
John

[Will Van Treuren]

Hi JQL,

Please search the forum for an answer to this question. I have personally answered this three times in the last two weeks and it has been asked at least twenty times in the forum.

Best,
Will

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