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

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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
Torst
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Location: The University of Melbourne, AUSTRALIA

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This is a good starting point: http://en.wikipedia.org/wiki/Gene_prediction

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
vikas0633
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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
ersgupta
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anybody has a solution for this error?
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Old 05-27-2015, 06:01 AM   #5
colindaven
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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
fahmida
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I also agree with Torsten and Colin. Augustus is much easier to deal with.
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