Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

    Comment


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

      Comment


      • #4
        anybody has a solution for this error?

        Comment


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

          Comment


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

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Exploring the Dynamics of the Tumor Microenvironment
              by seqadmin




              The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
              07-08-2024, 03:19 PM
            • seqadmin
              Exploring Human Diversity Through Large-Scale Omics
              by seqadmin


              In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
              06-25-2024, 06:43 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 07-19-2024, 07:20 AM
            0 responses
            25 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-16-2024, 05:49 AM
            0 responses
            41 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-15-2024, 06:53 AM
            0 responses
            45 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 07-10-2024, 07:30 AM
            0 responses
            42 views
            0 likes
            Last Post seqadmin  
            Working...
            X