Downloading 16S Sequences From Rdp And Greengenes

Question

[vijay]

Dear all,

Please can someone let me know how I could get all the 16 rDNA sequences available in Greengenes and Ribosomal database project websites.

I tried downlaoding from the http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/Reference_OTUs_for_Pipelines/ but I din't get the sequences.

Your responses are highly appreciated.

-Vijay

[Martin A Hansen]

You should really try harder.

[ken]

I had the exact same question and I signed up just to upvote these answers. Many thanks.

Answer 1

[satanicodr]

For the RDP. 1. Go to the website and click on "Browser": 2. Change the options if you want to include shorter sequences or low quality ones and click on "browse" 3. Click on "+" left to Bacteria if you want all the bacterial sequences, do the same for other groups if you are interested 4. Click on download and then check the options for formatting and then click your option under "Choose an alignment model for download" if you click on "Remove all gaps" the sequences will be unaligned

Answer 2

[Istvan Albert]

Go one level down and you can see the prealigned as well as the unaligned sequences:

http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/