Question

How To Download The16S Rdna Sequences Of All The Bacterial Species?

2

Entering edit mode

11.1 years ago

spandankeshav ▴ 80

I would like to download all the possible 16S rDNA sequences of bacterial species only. I tried Ribosomal Database Project (RDP) but I think it could be done only manually. I would like to donwload at once. So, is there any way to download all together at once?

• 5.8k views

ADD COMMENT • link updated 11.1 years ago by Daniel ★ 4.0k • written 11.1 years ago by spandankeshav ▴ 80

score 2 · Answer 1 · 2013-10-11

2

Entering edit mode

11.1 years ago

Asaf 10k

You can download the rRNA sequences from Rfam (family RF00177). Go to the Alignments tab (here: http://rfam.sanger.ac.uk/family/RF00177#tabview=tab2 ) and under Formatting options select Full, FASTA (ungapped) format and download and there you go. You should only change the U's to T's to get the DNA.

ADD COMMENT • link 11.1 years ago by Asaf 10k

0

Entering edit mode

Thanks a lot Asaf. It really helped. Cheers!

ADD REPLY • link 11.1 years ago by spandankeshav ▴ 80

score 2 · Answer 2 · 2013-10-11

2

Entering edit mode

11.1 years ago

Manu Prestat 4.1k

For RDP, you can find it in the resources tab (very top right). You should be able to find other downloads in similar DB such as greengenes or silva.

ADD COMMENT • link 11.1 years ago by Manu Prestat 4.1k

score 1 · Answer 3 · 2013-10-11

1

Entering edit mode

11.1 years ago

Daniel ★ 4.0k

The greengenes database allows you to download their 16S repository in a range of formats (including aligned):

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

ADD COMMENT • link 11.1 years ago by Daniel ★ 4.0k