Part-I : How to Download All Sequence of a Particular Organism from NCBI
Recently a reader of Bioinformatic-Made-Simple asked a question that
How to download nr database for a particular organism ? I have few thousands of sequences from which I want to do blastx and separate out the coding and non-coding sequences. pl. suggest me some solution.A similar question was also raised by A member of BioStar, a Bioinformatics forum. His question was that
I am doing annotation of a de novo sequenced non-model plant genome. Specifically, i am annotating the genome through blastx-ing the NCBI NR database. Obviously, it will be much faster if i can draw only plant protein sequences from the large NR database. So ia m wondering if there is a way to work out that. Hope it is possible.You can find the answer of different experts of the field HERE.
Since from question it is not clear that non redundant sequence of which organism or which database you are interested so let me suppose that it's NCBI database and sequence of any organism. So there may be two approach (at least for now) to extract the sequence of a specific organism form NCBI GeneBank.
- Go to the NCBI GENOME bowser page HERE.
- Choose the kingtom to which your organism belongs to.
- You can choose organisms by their group and sub group also.
- Click on the name of organism ( Abaca bunchy top virus genome, for example )
5. Step 4. will bring on the organism specific page of NCBI where you can get all information regarding that organism. Now click on the 'Protein' if you want to download protein sequence of that organism.
6. On the next page you will get the all protein sequence of that organism. Here click on 'Display setting' and choose the 'file format' and you done. So now you can download all protein sequence from NCBI database of a given organism. Alternatively, you can download all protein sequences by choosing the 'send to' option.
First of all, let me clear it that i am not a Bioinformatician. i am simple plant biology researcher who face problem in her daily research life and who bother to post solution of those problem on this webpage. That's it.