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) @k8hertNESCent Bioinformatics folks firstname.lastname@example.org
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: whats 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 SVAKate 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 searchingKate 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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