Taxonomy File for Silva Database

Commands in mothur
1

Hello,

It is imy first time to use Mothur!

I searched for the taxonomy file for Silva database :
http://www.arb-silva.de/fileadmin/silva_databases/current/Exports/SSURef_111_NR_tax_silva.fasta.tgz
but unfortunately I couldn’t find it.

the tax files in:
http://www.mothur.org/wiki/Silva_reference_files

are different in IDs than those in the first link.

Could any one help me?

Best Regards,
Hadidi

2

The “SILVA database” that we talk about is what you found in the Silva_reference_files link.

3

Dear Pshcloss,

Thank you for the reply.
I is it posible to create a taxonomy file by my own, if the taxonomy exist in the header of a fasta file?
for example, I have a fasta file whose header is like that:

AAAA02045240.678.2192 Bacteria;Bacteroidetes;Flavobacteria;Flavobacteriales;Flavobacteriaceae;Flavobacterium;Oryza sativa Indica Group
AGAGUUUGAU CCUGGCUCAG GAUGAACGCU AGCGGCAGGC CUAAUACAUG CAAGUCGGAC GGGAUCCGUC GGAGAGCUUG
CUCGAAGACG GUGAGAGUGG CGCACGGGUG CGUAACGCGU GAGCAACCUA CCUCUAUCAG GGGGAUAGCC UCUCGAAAGA

I tried to remove “>” and add “;” at the end of the line to be like the taxonomy format you have, but it gives me error saying:
‘AAAA02045240.678.2192’ is in your template file and is not in your taxonomy file. Please correct.

Your help is appreciated!

Best Regards,
Hadidi

4

Sure but there are some rules…

  1. No spaces in the taxonomy. You might replace them with “_”
  2. The taxonomy string needs to have a “;” at the end.
  3. The SILVA sequences have spaces in them between groups of 10 bases - remove those too.

Pat

5

I suggest to add sort option (for p-value) and cutoff (otu pairs higher than 0.05 p-value can be discarded) for otu.association command. I have over 1500 otus and the list is quite long, so it is hard to manually sort it.

6

Ok - but can’t you sort it in R, excel, command line, etc?