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  • 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?

  • #2
    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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    • #3
      I have same error. Let me know if you find a solution for glimmer

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      • #4
        anybody has a solution for this error?

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        • #5
          Augustus is easier people, I would recommend it over Glimmer.

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          • #6
            I also agree with Torsten and Colin. Augustus is much easier to deal with.

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