Unmoderated list for general discussion of bioperl modules, current and future efforts and related topics.

downloading 16s from NCBI

Hi,
    Is it possible to download all 16s sequences from NCBI?
I tried to look at Bio::DB::GenBank, but i am not sure if u can do it for
all 16s .

I would really appreciate if anyone can help me out.

Thanks
Shalabh

--

-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

headers

Florent Angly | 11 Feb 01:26

Re: downloading 16s from NCBI

Hi Shalabh,
There are specialized databases that contain only 16S rRNA genes, namely 
GreenGenes, RDP, Silva. You should have a look.
Regards.
Florent

On 11/02/12 04:30, shalabh sharma wrote:
> Hi,
>      Is it possible to download all 16s sequences from NCBI?
> I tried to look at Bio::DB::GenBank, but i am not sure if u can do it for
> all 16s .
>
> I would really appreciate if anyone can help me out.
>
> Thanks
> Shalabh
>
>

headers

Thomas Sharpton | 11 Feb 01:42

Re: downloading 16s from NCBI

Hi Shalabh,

Florent is correct about the specialized databases - they are great  
resources.

To answer your specific question about all 16S sequences in GenBank,  
see this webpage, which contains a 16S database download link:

http://www.ncbi.nlm.nih.gov/books/NBK82331/#Nov11.New_BLAST_16S_Prokaryotic_Ribosoma

Best,
Tom

On Feb 10, 2012, at 4:26 PM, Florent Angly wrote:

> Hi Shalabh,
> There are specialized databases that contain only 16S rRNA genes,  
> namely GreenGenes, RDP, Silva. You should have a look.
> Regards.
> Florent
>
>
> On 11/02/12 04:30, shalabh sharma wrote:
>> Hi,
>>     Is it possible to download all 16s sequences from NCBI?
>> I tried to look at Bio::DB::GenBank, but i am not sure if u can do  
>> it for
>> all 16s .
>>
>> I would really appreciate if anyone can help me out.

(Continue reading)