mothur

classify.otu with an updated NCBI reference taxonomy file


#1

Hello there.

I’ve been trying to classify my OTUs using Silva’s fasta/align files and silva.ncbi taxonomy files but I have faced different problems.

If I want to use the newest Silva release (v_132) I do not have any match between it and the NCBI taxonomy file, since (I presume), sequences’ names are not related between both files. Then, I tried to do the same but using the silva.bacteria.fasta file that is linked from the MiSeqSOP and classifying my OTUs with the same NCBI taxonomy file and I got good results. However, when I looked into the files details I can see that both silva.bacteria.fasta and related NCBI taxonomy file were created in 2012!

Is there any way to know if they are really so old?

And most important, is there any way to use Silva’s v132 release together with a NCBI taxonomic classification file?

Thanks a lot


#2

Hi there,

We didn’t include the NCBI taxonomy in the more recent SILVA releases. Our experience has been that the NCBI taxonomy is pretty dreadful in comparison to that provided by the RDP, SILVA, or greengenes. Is there a reason you need the NCBI taxonomy?

Pat


#3

Thanks Pat.

We are trying to get some information about our cyanobacterial OTUs further than the classification RDP brought us (i.e. Famili I, Gp V…) and we decided to try to use NCBI database in order to find out a more ‘classical’ taxonomic classification (Nostocales, Synechococcales…).

I do not know if there is another option to achieve this.

Regards
Miguel Ángel


#4

Any idea about this?

Thanks


#5

To be honest, RDP is about as classical as you can get since they use the official taxonomy from Bergey’s.

Pat