Re: [Cg-pipeline-users] additional predictor

[Gmail <kok...@gm...>]

Thanks Jay and Lee. It will be great if the option is added. I like prodigal for their better start prediction (from what i get for my test genome) and less false prediction for bacterial genome as claimed. Looking forward to the update, thanks!

On 02/08/2013, at 23:51, Lee Katz <ls...@gm...> wrote:

> I'm returning to the US and back to work on Aug 12. It sounds like a worthy addition. 
> 
>  I like prodigal but never bothered to put it in as an option. I think it could be something optional like genemark and would be preferred if not using genemark. In this way, CGP would still be able to have a majority for gene calling even if you don't have genemark. 
> 
> On Aug 2, 2013, at 15:43, Jay <jhu...@gm...> wrote:
> 
>> As far as I know, there is no convenient way of doing this. The run_prediction script would have to be modified to support running it and parsing the results.
>> 
>> On 02/08/2013 22:52, kok wrote:
>>> Is it possible for cg pipeline to include the results of other ab-initio predictor (eg. prodigal)? Is there any development for this function? 
>>> Or if I would like to use prodigal in place of genemark (if only two predictors allowed), can I convert the results of prodigal into genemark-like gm_out.lst file for cg pipeline's run_predict as a simple modification? 
>>> 
>>> - kok - 
>>> 
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