Question: AUGUSTUS principal isoform
1
gravatar for jomaco
3.9 years ago by
jomaco190
European Union
jomaco190 wrote:

Hi,

I have used AUGUSTUS for gene prediction.

It produces multiple isoforms for some genes. These are listed as XXXX.1, XXXX.2, XXXX.3 etc.

Which isoform can be taken to be the principal isoform i.e. the isoform used in further analysis?

I ask as it seems most genome papers only report functional descriptions for a single isoform.

--

However, I could report functional descriptions for all isoforms?

-  In lieu of this, at least for OrthoMCL clustering the selection of a principal isoform seems paramount (such that the output is not inundated with gene families consisting of matches between different isoforms of the same gene in the same species).

Until now I have simply gone with the isoform labelled ".1" - is this okay?

Thanks,

Jon.

 

 

 

ADD COMMENTlink written 3.9 years ago by jomaco190

Which species are you interested in?

ADD REPLYlink written 3.9 years ago by Denise - Open Targets4.7k

Don't think I'm supposed to say - but it's a species in the asterids if that helps, newly sequenced

ADD REPLYlink written 3.9 years ago by jomaco190

I see. I was thinking of APPRIS currently run for human, mouse, zebrafish, rat and others. Not sure if it would be useful for your study case. You may want to contact the authors.

ADD REPLYlink written 3.9 years ago by Denise - Open Targets4.7k
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