classify.seqs using the "trainset14_032015.pds.tax" as a reference file

Commands in mothur
1

Hi,

I found a problem using the “trainset14_032015.pds.tax” as a reference file.

For a sequence EU679419_S001240760 in the reference file,

“trainset14_032015.pds.tax” gives “Bacteria;Chloroflexi;Dehalococcoidetes;Dehalogenimonas;”
but the older version, “trainset9_032012.pds.tax” gives “Bacteria;“Chloroflexi”;“Dehalococcoidetes”;“Dehalococcoidetes”_order_incertae_sedis;“Dehalococcoidetes”_family_incertae_sedis;Dehalogenimonas;”

For a sequence in my data,
The former result in:
0.2.16 Chloroflexi
0.2.16.5 Dehalococcoidetes
0.2.16.5.1 Dehalogenimonas
0.2.16.5.1.1 unclassified
0.2.16.5.1.1.1 unclassified

The latter result in:
0.2.9 Chloroflexi
0.2.9.2 Dehalococcoidetes
0.2.9.2.1 Dehalococcoidetes_order_incertae_sedis
0.2.9.2.1.1 Dehalococcoidetes_family_incertae_sedis
0.2.9.2.1.1.1 Dehalogenimonas

That is, if I use “trainset14_032015.pds.tax”, the sequence is not classified at the genus level.
It seems that many sequences in the “trainset14_032015.pds.tax” have the same problem.

Thank you for your concern.

2

Hi,

If you have a problem with the RDP reference taxonomy, I would encourage you to bring it up with the RDP. We do very little to change the taxonomy. I would add that as time passes the community gets more information and taxonomic information changes so you should expect things like this to change.

Pat

3

Thank you for your kind reply, Dr. Pschloss,
I got it.