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  • From GeneBank to .GFF

    Hello everyone,

    I'm working with an organism that doesn't have a proper .gff annotated file available on NCBI. However, I can have a full GeneBank file. Does anyone know how to "convert" or extract the information in order to create .gff from GeneBank? My organism has about 52 genes (a virus), so I guess I could almost do it manually, but still...

    I have no true skills in programming, so... Any "easy" way of doing it?

    TP

  • #2
    Have a look at the following links:

    This program takes a sequence or sequences (alignment) as input in an unspecified format and converts the sequence(s) to a different user-specified format






    I have not used any of the scripts, though.

    Comment


    • #3
      I used the first one and wow... It seemed to work perfectly in a fraction of a second! I'll try to use it in HTseq-count, but I think it should work.

      Thanks a lot!!! I screened the web but missed this one!

      Comment


      • #4
        Hi There,
        I am having error while converting genebank file to gff format.
        I am using genbank2gff.pl perl script but i am getting following error

        ------------- EXCEPTION -------------
        MSG: type_map values must be scalar or CODE ref. You said: ARRAY(0x19c5050) for type: tRNA
        STACK Bio::SeqFeature::Tools::TypeMapper::map_types /usr/local/share/perl/5.14.2/Bio/SeqFeature/Tools/TypeMapper.pm:194
        STACK main::unflatten_seq genbank2gff.pl:891
        STACK toplevel genbank2gff.pl:395

        Can any body help me to find out the error..?

        Thanks in advance..

        Comment

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