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An ontology for
     transposable elements and
     other repetitive sequences
        in the age of genomics
                     Kate L Hertweck (NESCent)

Acknowledgements                         Find me:

J. Chris Pires and lab (U of Missouri)   @k8hert
NESCent Bioinformatics folks             k8hertweck@gmail.com
How can we effectively deal with repetitive elements?
●
     Repetitive sequences comprise a large portion of many genomes
●
     Characterization of repeats lags behind research of genes
    ●
        Descriptive biology: what's in a genome?
    ●
        Comparative biology: how and why do genomes vary?
    ●
        Ontology: how do we organize our conceptual framework for
        repeats?


 Class I: Retrotransposons   Class II: DNA transposons   Others
     LTR                         TIR                         Satellites
     LINE                        Crypton                     Simple repeats
     SINE                        Helitron
     ERV                         Maverick
     SVA



Kate Hertweck, TE ontology
What makes repeats different?
●
    There are many classification schemes for repeats
      ●
          RepBase, lineage specific databases
      ●
          Organization based on evolutionary relationships (Wicker et al 2007)
●
    Repeats are difficult!
      ●
          Breadth of knowledge growing, but many black boxes remain
      ●
          Many copies throughout genome
      ●
          Difficulty in identification and annotation
●
    Lots of metadata necessary
      ●
          Organism sequenced: taxonomy, voucher
      ●
          Method of sequencing: next gen, sequence length, coverage
      ●
          Assembly method: ab initio, de novo
      ●
          Annotation approach: library, motif searching

Kate Hertweck, TE ontology effects of junk DNA
               Evolutionary
Formalizing structure
 ●
     Developing the ability to summarize and compare repeat
       compliments from genomes of multiple organisms
 ●
     What is common between repetitive elements and
       genes/proteins/morphology?
 ●
     Does the age of a repeat matter? Fossils, inactivated, active but not
       inserting
 ●
     Relevant projects:
       ●
            Comparative Data Analysis Ontology (NESCent EvoInfo)
       ●
            Homology Ontology (Robison-Rechavi Lab)
 ●
     Suggestions welcome!




Kate Hertweck, TE ontology effects of junk DNA
               Evolutionary

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iEvoBio Hertweck presentation 2012

  • 1. An ontology for transposable elements and other repetitive sequences in the age of genomics Kate L Hertweck (NESCent) Acknowledgements Find me: J. Chris Pires and lab (U of Missouri) @k8hert NESCent Bioinformatics folks k8hertweck@gmail.com
  • 2. How can we effectively deal with repetitive elements? ● Repetitive sequences comprise a large portion of many genomes ● Characterization of repeats lags behind research of genes ● Descriptive biology: what's in a genome? ● Comparative biology: how and why do genomes vary? ● Ontology: how do we organize our conceptual framework for repeats? Class I: Retrotransposons Class II: DNA transposons Others LTR TIR Satellites LINE Crypton Simple repeats SINE Helitron ERV Maverick SVA Kate Hertweck, TE ontology
  • 3. What makes repeats different? ● There are many classification schemes for repeats ● RepBase, lineage specific databases ● Organization based on evolutionary relationships (Wicker et al 2007) ● Repeats are difficult! ● Breadth of knowledge growing, but many black boxes remain ● Many copies throughout genome ● Difficulty in identification and annotation ● Lots of metadata necessary ● Organism sequenced: taxonomy, voucher ● Method of sequencing: next gen, sequence length, coverage ● Assembly method: ab initio, de novo ● Annotation approach: library, motif searching Kate Hertweck, TE ontology effects of junk DNA Evolutionary
  • 4. Formalizing structure ● Developing the ability to summarize and compare repeat compliments from genomes of multiple organisms ● What is common between repetitive elements and genes/proteins/morphology? ● Does the age of a repeat matter? Fossils, inactivated, active but not inserting ● Relevant projects: ● Comparative Data Analysis Ontology (NESCent EvoInfo) ● Homology Ontology (Robison-Rechavi Lab) ● Suggestions welcome! Kate Hertweck, TE ontology effects of junk DNA Evolutionary