[Bioperl-l] downloading 16s from NCBI

Thomas Sharpton thomas.sharpton at gmail.com
Fri Feb 10 19:42:58 EST 2012


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.
>>
>> Thanks
>> Shalabh
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



More information about the Bioperl-l mailing list