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Old 10-09-2012, 10:13 PM   #1
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Location: USA

Join Date: Jul 2012
Posts: 8
Default Eukaryotic orf finder

Hi All,

I am looking for Eukaryotic orf finder algorithm/source code. I am trying to build training model for unknown eukaryotic genome using Glimmerhmm. I need collect orf's for the Glimmerhmm training model. So I did BLASTp against known eukaryotic protein sequences (closest neighbour to the unknown eukaryote) but am unable to build the training model with resultant orf's. The error I get after trainGlimmerhmm is:
Training data created successfully! Check exons.dat and seqs for accuracy.

Acceptor sites for training: 18292
False acceptor sites for training: 853751
Donor sites for training: 18219
False donor sites for training: 672464

ERROR 69: /GlimmerHMM/train/score exited funny: 35584

If this process of building training model is right then can anyone help me with this situation. If not then what can I do to build training model? Should I look for acceptor and donor sites in the upstream and downstream of the orf's I got in blastp?
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Old 10-13-2012, 12:41 AM   #2
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Location: The University of Melbourne, AUSTRALIA

Join Date: Apr 2008
Posts: 275

This is a good starting point:

Then look at the software in the References section. Augustus might be nicer.
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Old 10-14-2012, 07:40 AM   #3
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Location: denmark

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I have same error. Let me know if you find a solution for glimmer
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Old 05-26-2015, 02:12 AM   #4
Location: India

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Posts: 26

anybody has a solution for this error?
ersgupta is offline   Reply With Quote
Old 05-27-2015, 06:01 AM   #5
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Location: Germany

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Augustus is easier people, I would recommend it over Glimmer.
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Old 05-27-2015, 04:18 PM   #6
Location: Australia

Join Date: Aug 2010
Posts: 54

I also agree with Torsten and Colin. Augustus is much easier to deal with.
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