[maker-devel] Evidences in fasta format but be alignment in every run?

[Carson Holt]

MAKER is restartable. As long as you run each time in the same location, it can reuse existing alignments from the previous run. You also only need to train on ~10MB of the genome depending on gene density. Target size should be 300-400 genes.

If you follow this GMOD wiki, this is demonstrated (you can also watch video - link as top of page - to see it being done) —> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Training_ab_initio_Gene_Predictors <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Training_ab_initio_Gene_Predictors>

—Carson



> On Feb 10, 2017, at 8:50 AM, Quanwei Zhang <qwzhang0601 at gmail.com> wrote:
> 
> Hello: 
> 
> I am annotating a new genome using Maker. I have RNA-seq assembly and protein sequences (from other organisms) in fasta format. Since I need to train gene finders, so I have to run Maker several times. I think the aligning process between the transcript assembly (protein sequences) and the genome assembly may be time consuming. So I wonder whether I can save such alignment in the first run, and then make use of such alignment in the following runs?
> 
> Thanks
> 
> Best
> Quanwei
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