[maker-devel] Plastid annotation

[Daniel Ence]

Hi Shane, I'm not familiar with anyone using MAKER to annotate organellar genomes. My guess is that there might be a more specialized pipeline for this purpose.

Glimmer isn't integrated into MAKER, but if you can get a gff3 file from it, you can pass those predictions to MAKER. The only difference between passing predictions and running it within MAKER is that MAKER will generate and pass "hints" based on the blast alignments to its internal predictors. MAKER can't do that with predictions generated externally.

Thanks,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of Shane Brubaker [sbrubaker at solazyme.com]
Sent: Wednesday, January 08, 2014 11:10 AM
To: maker-devel at yandell-lab.org
Cc: Aren Ewing
Subject: [maker-devel] Plastid annotation

Hi, we are embarking on a project to annotate several plastids.  We want to do all the work in-house though (i.e. we don’t want to use a web service) and we would like to use MAKER if possible.

As you know the plastid is essentially bacterial, so I get the impression that it would not be appropriate to use Augustus or SNAP on it, is that correct?

Is it possible instead to use Glimmer within MAKER?

I was wondering if anyone has suggestions on 1) how to use MAKER with organellar genomes and 2) other general organellar annotation piplelines that people have found useful (and useable) that are downloadable to a local installation.


Thanks,
Shane Brubaker

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