Question: How can I download all NR fasta sequences corresponting to the same specie from NCBI?
0
gravatar for Neuls
2.2 years ago by
Neuls0
Neuls0 wrote:

Hi,

I'm interested on comparing 16S rna among some species so I'd like to download all NR_ fasta sequences from NCBI 16Sdatabase corresponding to a specie of interest. I have been reading about Enterz but I wonder if it can be done easly from a webrowser. So far I got sequences from Silva database Ref but they contain sequence form contigs and so on..

Thank you

entrez nr 16s ncbi • 1.1k views
ADD COMMENTlink written 2.2 years ago by Neuls0

At https://www.ncbi.nlm.nih.gov/nuccore build your query like this:

"YOUR-SPECIES-NAME-HERE"[Organism]

Choose some parameters on the right side, e.g. just RefSeq or limit by length, or don't.

Then click send, "Choose Destination" -> File -> Fasta, your download will start automatically.

If your species is not a model species then you might be lucky and be able to download all sequences this way. Otherwise it will have to be Entrez or you download all sequences from the same DB (e.g. Invertebrates or Plants/Fungi or ...) from the NCBI FTP and then do manual (script-based) filtering...

ADD REPLYlink written 2.2 years ago by cschu1811.7k
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