Question: How to retrieve all fasta sequences using Assembly/BioProject ID using Entrez Programming Utilities
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fengzys • 50 wrote:
I am trying to download all the viral and bacterial genome (in Genome database), I have used Entrez utilities. Firstly, Esearch was use to retrieve all the viral Genome UID, which was then translated to nuccore gi number by Elink, some gi number corresponds to the parental description of a WGS projects, thus the fasta sequence can not obtained by efetch directly, by parsing the gb output of these gi, I can get the accession number, but this is very tedious. Is there a way to get all the sequences belongs to a Assembly or Bioproject? (Elink could translate genome UID to Assembly or BioProject ID). Thanks for your time.
