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  • Download RefSeq .gb files based on accession number

    Hi,
    I have a list of genomic accession numbers (e.g. NG_007941.2, NG_009018.1).
    I'd like to download .gb files based on these identifiers.

    Manually, I can type it in NCBI and I got the page, e.g.
    http://www.ncbi.nlm.nih.gov/nuccore/...report=genbank

    then I click: "send", Choose Destination "File", Format: GenBank "CreateFile".

    Is there any automatic way to obtain such files?

    I've tried BioPerl and Bio:B::EUtilities, but I don't see any clear way how to do this.

  • #2
    You can use the Entrez e-utilities. See this page and choose your preferred method.

    Comment


    • #3
      Originally posted by GenoMax View Post
      You can use the Entrez e-utilities. See this page and choose your preferred method.

      https://www.ncbi.nlm.nih.gov/guide/howto/dwn-records/
      Thank you very much!
      I've found this http://www.ncbi.nlm.nih.gov/books/NB...trieving_large
      after little modifications, it does exactly what I need!

      Comment


      • #4
        @GenoMax, do you know if there is any robust way to download sequences of pseudogenes of the gene?

        I have already GBK RefSeqGene sequences and additionaly I'd like to have corresponding pseudogenes sequences, for example:
        NF1.gbk - GBK validated by RefSeqGene, downloaded based on accession number
        NF1_p1.gbk - pseudogene 1
        NF1_p2.gbk - pseudogene 2

        Comment


        • #5
          Originally posted by thedamian View Post
          @GenoMax, do you know if there is any robust way to download sequences of pseudogenes of the gene?

          I have already GBK RefSeqGene sequences and additionaly I'd like to have corresponding pseudogenes sequences, for example:
          NF1.gbk - GBK validated by RefSeqGene, downloaded based on accession number
          NF1_p1.gbk - pseudogene 1
          NF1_p2.gbk - pseudogene 2
          How about adding "pseudo" or "pseudogene" to your search terms. e.g. NF1 AND Pseudogene (note: AND has to be in capital).

          Comment

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