2008 Genomics Course

    Notices and Announcements

    • I added some goals (for grading purposes).  gribskov 22 October 2008

    Instructors

    Course Materials

    Lectures

    Gribskov

    1. PDF Genome Assembly
    2. PDF Genome Assembly
    3. PDF Gene finding (finding sites & motifs)
    4. PDF Gene finding (BLAST, HMM)
    5. missing
    6. PDF
    7. PDF Protein Families/Protein Strudcture Prediction

    Reading

    • PDF Genome assembly forensics: finding the elusive mis-assembly
    • PDF An Introduction to Hidden Markov Models
    • PDF Gene identification in novel eukaryotic genomes by self-training algorithm
    • PDF In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists
    • PDF Evaluation of five ab initio gene prediction programs for the discovery of maize genes
    • PDF Comparative genomics as a tool for gene discovery
    • PDF Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment
    • PDF NETWORK BIOLOGY:UNDERSTANDING THE CELL’S FUNCTIONAL ORGANIZATION

    Genome Annotation Projects

    • Sequences and progress from annotation groups will be posted here. 
    • Please sign your work by using 4 "~" (tildes).  for me the four tildes  become 'gribskov 09 October 2008'.
    • If you change the title (e.g., smo9 project) this will create a new page with that name.  That's OK, but update the link below in the Sequence files section
    • See the user manual for help with creating and editing pages (yes you can)

    Expectations for your site

    • BLAST results of genomic DNA vs DNA and protein databases => candidate genes
    • Gene Predictions by at least 2 methods
    • List of "real genes" with
      • exon / UTR coordinates with comments
      • predicted gene function
      • anything intersting about the gene
    • List of probably pseudogenes and artifacts
    • identify non-gene elements, if present (transposons, degenerate sequence, etc.)
    • Plot of genes and other elements in genomics segment

    Sequence files

    Each is approximately 100kb.  Sequences are from Selaginella moellendorfii.  To indicate your choice of project, add the names of each team after the project by having each partner edit this page and add four tildes(~).  The wiki will automatically replce the tildes with your name and the current date (3 would get just your name)Click on the project page link and start adding material to your page.

    example

    Suggestions

    • See the user manual for help with creating and editing pages
    • To get a sense of how to use the wiki
      • Add something to your personal page (see my page at upper left)
      • Use your personal page as a to-do list
      • Restrict access to your to-do list


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    Files 23

    FileSizeDateAttached by 
     04barabasi_NatureRev.pdf
    No description
    375.39 kB12:09, 3 Nov 2008gribskovActions
     05genemark.pdf
    Gene identification in novel eukaryotic genomes by self-training algorithm
    777.14 kB08:37, 9 Oct 2008gribskovActions
     08Agry600_1.pdf
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    551.61 kB10:54, 7 Oct 2008gribskovActions
     08Agry600_2.pdf
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     08Agry600_3.pdf
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    578.29 kB08:32, 9 Oct 2008gribskovActions
     08Agry600_4.pdf
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     08Agry600_6.pdf
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    343.88 kB08:54, 28 Oct 2008gribskovActions
     08Agry600_8.pdf
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    2.51 MB08:54, 28 Oct 2008gribskovActions
     08phillipy_genomeBiol.pdf
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    638.62 kB08:52, 9 Oct 2008gribskovActions
     414.pdf
    In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists
    289.84 kB08:39, 9 Oct 2008gribskovActions
     compgenomics.pdf
    Comparative genomics as a tool for gene discovery
    210.52 kB08:37, 9 Oct 2008gribskovActions
     introtohmm.pdf
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    789.51 kB10:40, 7 Oct 2008gribskovActions
     Plant_Molecular_Biology_vol57pp445-460.pdf
    Evaluation of five ab initio gene prediction programs for the discovery of maize genes
    450.56 kB08:39, 9 Oct 2008gribskovActions
     promoter_pred.pdf
    Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment
    917.8 kB08:37, 9 Oct 2008gribskovActions
     smo1.fa
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    100.96 kB13:56, 9 Oct 2008gribskovActions
     smo2.fa
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    97.04 kB13:56, 9 Oct 2008gribskovActions
     smo9.fa
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    126.19 kB07:39, 10 Oct 2008gribskovActions
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