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?
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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