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Old 09-05-2014, 06:20 AM   #1
fefe89
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Default Make a blast on a specific organism (blast+)

Hi

I would like to make a blast on a specific organism.


Does anyone know how to set blastp (blast+) in order to obtain results only from a specific organism?

In the html blast you can select the organism (and corresponding taxa ID), I assume it should work in a similar fashon

Thank you
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Old 09-05-2014, 07:08 AM   #2
Cytosine
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The most straightforward approach for this is to set up a local database for your organism.

As for remote queries on NCBI's servers, well... AFAIK (correct me if I'm wrong) blast+ suite does not support filtering with taxids yet.
You can try using the entrez_query string to subset the results, which should do a good job at filtering your blast results, though I'm not sure how good that approach is compared to a straightforward taxid filtering.
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Old 09-05-2014, 09:41 AM   #3
fefe89
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Quote:
Originally Posted by Cytosine View Post
The most straightforward approach for this is to set up a local database for your organism.

As for remote queries on NCBI's servers, well... AFAIK (correct me if I'm wrong) blast+ suite does not support filtering with taxids yet.
You can try using the entrez_query string to subset the results, which should do a good job at filtering your blast results, though I'm not sure how good that approach is compared to a straightforward taxid filtering.
Thank you for your reply.

The problem is that I have a large amount of metagenomic data and I need to extract only the ORFs that have a viral origin.

I'm pretty new of the bioinformatic world.

Is there any way to take all the genes that have a viral origin from NCBI and make a sort of viral database?
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Old 09-05-2014, 11:56 AM   #4
Cytosine
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Quote:
Originally Posted by fefe89 View Post

Is there any way to take all the genes that have a viral origin from NCBI and make a sort of viral database?
Of course, you can do that with Genbank.

Perform a query to find all viral sequences and once you get the results, select in the dropdown menu:
- send to
- File
- format FASTA
- create file

You can use the resulting fasta file then to make your blast database.
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Old 09-05-2014, 11:06 PM   #5
fefe89
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Quote:
Originally Posted by Cytosine View Post
Of course, you can do that with Genbank.

Perform a query to find all viral sequences and once you get the results, select in the dropdown menu:
- send to
- File
- format FASTA
- create file

You can use the resulting fasta file then to make your blast database.
Thank you very much!
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