An ontology for     transposable elements and     other repetitive sequences        in the age of genomics                ...
How can we effectively deal with repetitive elements?●     Repetitive sequences comprise a large portion of many genomes● ...
What makes repeats different?●    There are many classification schemes for repeats      ●          RepBase, lineage speci...
Formalizing structure ●     Developing the ability to summarize and compare repeat       compliments from genomes of multi...
Upcoming SlideShare
Loading in …5
×

iEvoBio Hertweck presentation 2012

387 views

Published on

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

0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
387
On SlideShare
0
From Embeds
0
Number of Embeds
2
Actions
Shares
0
Downloads
4
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

iEvoBio Hertweck presentation 2012

  1. 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) @k8hertNESCent Bioinformatics folks k8hertweck@gmail.com
  2. 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: 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
  3. 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 searchingKate Hertweck, TE ontology effects of junk DNA Evolutionary
  4. 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

×