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  • How to fetch any older version ACCs from NCBI using programming language?

    For example: I want to get the genomic coordinates of NR_046018.1, which has been updated and removed from the current release of NCBI databases.
    Then,how can I retrieve the record using EUtils like API?

    Or maybe, anyone can supply another fresh way to deal with this kind of work?
    Any suggestions?

    Thanks in advance.

  • #2
    Saddly, no answer, then maybe I should do it another way, does anyone know where can I find an accession number dependent version update notes on NCBI?

    e.g. NM_001604.4 -> NM_001604.5 ... anything changed?

    Comment


    • #3
      In BioPython you can specify the accession with the decimal points and get the two different records:
      Code:
      >>> from Bio import Entrez
      >>> Entrez.email = '[email protected]'
      >>> handle1 = Entrez.efetch(db="nucleotide", id = "NR_046018.1", rettype = "gb")
      >>> print handle1.read()
      ...older version - sequence ends gtttct...
      >>> handle2 = Entrez.efetch(db="nucleotide", id = "NR_046018.2", rettype = "gb")
      >>> print handle2.read()
      ...newer version - sequence ends gtttctg...
      That is the only eutils wrapper I have experience with but I would think anything would work like that.

      Comment


      • #4
        Thanks cliffbeall
        I understand that EUtils can fetch older version of ACC from nucl db of NCBI, even in
        genbank or xml format, but I cannot find the genomic coords from any of the returned files.
        The genomic coords of current version of ACC can be obtain by esearch & efetch from db:gene element:Gene-commentary_genomic-coords easily, But this's not available for older version.

        I know that the final solution is to run `splign` from sequences, but it's rather a tough way for whole genome and thousand of genes.

        Any other suggestions?

        Comment


        • #5
          Sorry, I guess I misunderstood the question.

          I don't know how to do what you want, it has to do with links between nucl and gene databases.

          Comment


          • #6
            It's not your fault, my misleading indeed.
            Thanks cliffbeall.
            Waiting for any further suggestions ...

            Comment

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