[maker-devel] Using GlimmerHMM with MAKER

[Shaun Jackman]

Thanks, Carson. That helps. I'm trying to do a completely ab initio gene
annotation without any est or protein homology evidence, at least for now.
The GFF file produce by maker is empty. How do I carry the GlimmerHMM
pred_gff (or model_gff) annotations through to the end? Ultimately, I'd
like to merge annotations from multiple ab initio predictions.

Cheers,
Shaun


On 10 April 2014 11:53, Carson Holt <carsonhh at gmail.com> wrote:

> Make sure it's not GTF or GFF2, but if it is GFF3 You can substitute match
> for mRNA and match_part for CDS.  Then it will be interpreted as a two
> level alignments feature which can be given to pred_gff.
>
> --Carson
>
> From: Shaun Jackman <sjackman at gmail.com>
> Reply-To: Shaun Jackman <sjackman at gmail.com>
> Date: Thursday, April 10, 2014 at 12:34 PM
> To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Using GlimmerHMM with MAKER
>
> The GlimmerHMM gene prediction software outputs a GFF file that includes
> mRNA and CDS features, but it does not include gene or exon features, and
> so it does not appear to be working with MAKER. Has anyone else used
> GlimmerHMM with MAKER, and how did you deal with this issue?
>
> Cheers,
> Shaun
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