[ensembl-dev] Getting GFF3 files from Ensembl MySQL database.

Paul Linehan linehanp at tcd.ie
Thu Dec 19 13:42:36 GMT 2013


Sorry - forgot to change subject on previous thread! Please use
this one to respond.


Paul...


> Hi all,
>
> I'm new to the Ensembl, so please forgive me if this question is
> misplaced.
>
>
> I've just downloaded and installed the Ensembl MySQL database for C. elegans.
>
> I was wondering if it's possible to generate GFF3 files from this data
> automatically using Java (has to be Java)?
>
> I know that there is GTF available here:
> http://www.ensembl.org/info/data/ftp/index.html
>
> And a script (with caveats!) available here:
> http://gmod.org/wiki/GFF (but in Perl!)
>
>
> What I was wondering, if there a JEnsembl/BioJava (or other) tool for
> generating GFF3 files from the data in an Ensembl database?
>
>
> Any ideas, refs, URLs, suggestions appreciated.
>
>
>
> Paul...
>
>
> --
>
> linehanp at tcd.ie
>
> Mob: 00 353 86 864 5772




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