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  • from CDS/genome sequences to gff file

    I inherited the database of CDS and genome. Wonder if there is an easy way to generate the gff3 file or any version of gff file.

    Thanks.

  • #2
    Hi,
    Which database are you refering to? You make have to look carefully as some databases provide annotation files which would have information about location of the CDS on the genome. It may be of another type which you will have to convert to gff3.
    Should you not find it, you may have to align the CDS to the genome. However, this option has some limitations:
    - Parameters for aligning them may not gaurantee their exact locations (e.g paralogs)
    - Some may not align eventhough you are sure they are from that genome.

    In anycase, this would be the lizard over the croccodile choice.

    Hope this helps!

    Comment


    • #3
      Thank you for your reply.

      The databases are sequence databases (both are fasta files)

      Comment


      • #4
        Hi capricy,

        As I am also in almost similar situation like you (I've protein and genome, looking to generate gff), I am interested to know the approach you take to achieve it ...

        Thanks.

        Comment


        • #5
          Hi capricy,
          I was requesting for the name of the database. Can you also provide the URL to the data-sets which you've downloaded? I should take a look at it. Like I mention earlier, in the absence of such a file, you may have to align the CDS to the genome with your prefered tools

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          • #6
            Hi capricy,
            I was requesting for the name of the database. Can you also provide the URL to the data-sets which you've downloaded? I should take a look at it. Like I mention earlier, in the absence of such a file, you may have to align the CDS to the genome with your prefered tools
            @fahmida, this goes same for you. There should be information about the CDS that gave those proteins. It is 'confortable' to align CDS than proteins.

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            • #7
              Hi, Apexy,

              My databases came from the collaborator, not downloadable yet, and they are plain sequence text. As you pointed out, aligning itself has issues. So we decided to use other databases with available gff files.

              Thanks a lot for your reply.

              Capricy

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