Question: Greengene : what is the "99" in OTU description?
0
gravatar for sacha
2.7 years ago by
sacha1.8k
France
sacha1.8k wrote:

Hi,

From greengene database, I don't understand the meaning of "99" with OTU description. For exemple, in the stat file, I have the following lines :

Total number of OTUs:
$ grep -c "^>" *.fasta
61_otus.fasta:22
64_otus.fasta:33
67_otus.fasta:53
70_otus.fasta:125
73_otus.fasta:267
76_otus.fasta:554
79_otus.fasta:1165
82_otus.fasta:2496
85_otus.fasta:5088
88_otus.fasta:10544
91_otus.fasta:22090
94_otus.fasta:46256
97_otus.fasta:99322
99_otus.fasta:203452

Same with the file

  gg_13_5_otus_99_annotated.tree.gz .

So, what does the number 99 mean ? Thanks !

taxonomy greengenge otu • 2.0k views
ADD COMMENTlink modified 2.6 years ago by timodonnell80 • written 2.7 years ago by sacha1.8k
1
gravatar for Lars Juhl Jensen
2.7 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

My guess would be that means 99% sequence identity. As far as I know, 97% and 99% are two fairly common sequence identity cutoffs for OTU clustering based on 16S rRNA.

ADD COMMENTlink written 2.7 years ago by Lars Juhl Jensen11k
1
gravatar for timodonnell
2.6 years ago by
timodonnell80
United States
timodonnell80 wrote:

I also ran into this question, and looks like the answer by Lars above is essentially correct. In particular from this thread on the QIIME forum:

To clarify the 97_otus.fasta rep_set was created by clustering all the sequences in the Greengenes database into 97% identity clusters and then a representative sequence was chosen from each of those clusters to be used to create the 97_tree and 97_taxonomy. Therefore each OTU id in the 97_otus.fasta file I see that representative sequence.

ADD COMMENTlink written 2.6 years ago by timodonnell80
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