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  • Genbank feature annotation?

    Would anyone by chance know how to create a Feature Annotation to a sequence? that's the part in the Genbank record right before the actual sequence. The feature annotation in Genbank looks like this:

    D-loop complement(join(16029..16570,1..579))

    tRNA 579..649
    /product="tRNA-Phe"
    rRNA 650..1603
    /product="12S ribosomal RNA"
    tRNA 1604..1672
    /product="tRNA-Val"
    rRNA 1673..3230
    /product="16S ribosomal RNA"
    tRNA 3231..3305
    /product="tRNA-Leu"
    /note="codons recognized: UUR"
    gene 3308..4263
    /gene="ND1"
    CDS 3308..4263

    etc.

    Is there some (preferably free...) software where I can enter my sequence and then have the annotation come up? Either in this format, or even better, 5 column tab delimited format...Or any format.
    (This is the part that annotates where to find the different genes etc in the sequence).

    thanks everyone. I think i better post this in its own message, too, so that it doesn't get lost.

    Sammi

  • #2
    You may use the tool at

    http://www.ianlogan.co.uk/checker/submission_maker.htm

    The procedure is laid out pretty good in the instructions at the bottom of the above websites.

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    • #3
      That's unfortunately not what I need. I had already been to Ian Logan's site. It's a nice program but there's no way to get that Feature Annotation I need by running it thru his program. (Also note that his .seq file generated does not contain all the fields possible within Bankit, if you've ever been to that site).
      Thanks anyway for replying. Am still loking: if anyone out there does know a program I can use to get that feature annotation, I would appreciate if u could post (or maybe someone whose used BankIt would be great too). thanks.

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      • #4
        Sorry for my initial naive response. I just thought you were trying to submit a record.

        Below is the URL explaining the perl interface for the Feature-Annotation data:
        http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

        You can contact the authors shown above if you're not perl programmer and need a program since the above is only a perl module interface document.
        Last edited by thetick; 4 October 2011, 12:18 AM.

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        • #5
          Way cool! I will check this out now.

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          • #6
            I just wrote a long reply. when I was done and hit post it kicked me back to the log in screen even tho I was already logged in. logged in again and got a blank screen. bottom line is it erased that entire long message explaining why i'mbstill stuck and exactly what it is i'm trying to do.

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