Embed Size (px)
Citation preview
An ontology for transposable elements and other repetitive sequences
in the age of genomicsKate L Hertweck (NESCent)
Acknowledgements
J. Chris Pires and lab (U of Missouri)NESCent Bioinformatics folks
Find me:
How can we effectively deal with repetitive elements?
Kate Hertweck, TE ontology
● 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: RetrotransposonsLTRLINESINEERVSVA
Class II: DNA transposonsTIRCryptonHelitronMaverick
OthersSatellitesSimple repeats
What makes repeats different?
Kate Hertweck, Evolutionary effects of junk DNAKate Hertweck, TE ontology
● 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
Formalizing structure
Kate Hertweck, Evolutionary effects of junk DNAKate Hertweck, TE ontology
● 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!
