Powerpoint for presentation on transposable element ontology for iEvoBio in Ottawa, July 2012 (see associated abstract)

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?
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Repetitive sequences comprise a large portion of many genomes
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Characterization of repeats lags behind research of genes
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Descriptive biology: what's in a genome?
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Comparative biology: how and why do genomes vary?
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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?
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There are many classification schemes for repeats
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RepBase, lineage specific databases
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Organization based on evolutionary relationships (Wicker et al 2007)
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Repeats are difficult!
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Breadth of knowledge growing, but many black boxes remain
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Many copies throughout genome
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Difficulty in identification and annotation
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Lots of metadata necessary
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Organism sequenced: taxonomy, voucher
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Method of sequencing: next gen, sequence length, coverage
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Assembly method: ab initio, de novo
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Annotation approach: library, motif searching
Kate Hertweck, TE ontology effects of junk DNA
Evolutionary

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