Gene discovery

point blank · 04-25-2013, 10:25 PM

Are there any tools available which will look at reference sequence and list out all the possible locations that can be potentially genes? or alternatively is there a tool that can take a sequence as input and predict if it can be a gene?

kbradnam · 04-25-2013, 10:34 PM

I think you are really talking about 'ab initio' gene prediction (see https://en.wikipedia.org/wiki/Gene_prediction) and there are a lot of tools that can do this.

Maybe Maker could be useful to you: http://www.yandell-lab.org/software/maker.html

point blank · 04-25-2013, 10:39 PM

Quote:

Originally Posted by kbradnam

I think you are really talking about 'ab initio' gene prediction (see https://en.wikipedia.org/wiki/Gene_prediction) and there are a lot of tools that can do this.

Maybe Maker could be useful to you: http://www.yandell-lab.org/software/maker.html

kbradnam, Thanks a ton for this real quick reply.. This is exactly what I am looking for. Has anyone run these tools on entire human reference say hg18 or hg19?

rhinoceros · 04-25-2013, 11:32 PM

Quote:

Originally Posted by point blank

Has anyone run these tools on entire human reference say hg18 or hg19?

Almost certainly yes.

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04-25-2013, 10:25 PM	#1
point blank Junior Member Location: India Join Date: Apr 2013 Posts: 3	Gene discovery Are there any tools available which will look at reference sequence and list out all the possible locations that can be potentially genes? or alternatively is there a tool that can take a sequence as input and predict if it can be a gene?

04-25-2013, 10:34 PM	#2
kbradnam Member Location: Davis, CA Join Date: May 2011 Posts: 53	I think you are really talking about 'ab initio' gene prediction (see https://en.wikipedia.org/wiki/Gene_prediction) and there are a lot of tools that can do this. Maybe Maker could be useful to you: http://www.yandell-lab.org/software/maker.html