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Old 04-25-2013, 10:25 PM   #1
point blank
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Default 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?
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Old 04-25-2013, 10:34 PM   #2
kbradnam
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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
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Old 04-25-2013, 10:39 PM   #3
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Quote:
Originally Posted by kbradnam View Post
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?
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Old 04-25-2013, 11:32 PM   #4
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Quote:
Originally Posted by point blank View Post
Has anyone run these tools on entire human reference say hg18 or hg19?
Almost certainly yes.
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