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Filter nt database remotely

How can I filter nt database remotely, to include only some taxa? (I'm sorry if this is a naive question)

nt biopython blast
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updated by GenoMax GenoMax • written by anasofiamoreira94 anasofiamoreira94

1 answer

You can't do this (in the sense of filter remotely and download only what you need).

  1. You could run a remote blast search at NCBI with a valid entrez query (simulating remote filtering).
  2. You could also search NCBI with species/genes of interest and download the search sequences from the web page results to create a local sequence search database from those.
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written by GenoMax GenoMax

Yes. That is the kind of search term you will use as shown in the search box. Here is a full list of those terms

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written by GenoMax GenoMax

I'm using entrez, and I did this command: Entrez.esearch(db='nucleotide',term="Mammals AND cox1[Gene]", idtype='acc') and it counts me 61818, but when I list the IDS I only get some of them. Is this the maximum number of IDS to print, or the result by itself?

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written by anasofiamoreira94 anasofiamoreira94

Looks like you are doing this in python. Add retmax=1000000 to get all results.

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written by GenoMax GenoMax

That worked, thanks that worked. I want to delete the fasta sequences of that query so I did this line: Entrez.efetch(db='nucleotide', id=id_list,retmode="fasta"), but I can't retrive the fasta sequences.

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written by anasofiamoreira94 anasofiamoreira94

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