Part- II : How to Download nr Database For a Particular Organism

Yesterday, I explain a method to download nr database for a particular organism. In this post let us discuss another approach to download non redundant sequence of a given organisms form NCBI. Let me clear that I love the first method because of its simplicity. Steps of this method are as follows

Also readPart- I : How to Download nr Database For a Particular Organism 

  1. Go to the NCBI home page HERE. 







2. Choose PROTEIN as target database and Search with all [filter] query
3. On the result page, you will get the list of organism and the number of sequences of that organism in bracket.

4. Click on the list/tree to change the view.
5. Choose the taxonomic group to which your organism belong to. (For example, flowering plant if I am looking for Arabidopsis)

6. You can narrow down the classes 


7. Finally You can export you sequences as I explain in step 6 of my previous tutorial.

I know that there may be so many other easier method to download nr database for a specific organism.  If you know anyone, please do share with us




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2 comments:

  1. UnknownDecember 16, 2015 at 4:56 PM

    Hi,

    if I use PROTEIN as target database and search with "all [filter]" query I cannot get the taxonomic tree like in your example. Do I have to change something in the display settings?

    Thanks a lot

    ReplyDelete
    Replies
    1. संजयDecember 16, 2015 at 6:21 PM

      Hi,
      Actually there are two way to see these data either as a list or as a tree. By default it will come as a list so to get the data as a tree you have to click on '
      Results by 'Top Organisms [Tree] '

      Delete

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