qmul sbcs SBMS035

1. Genome Bioinformatics
y.wurm@qmul.ac.uk

2. © Alex Wild & others

4. Atta leaf-cutter ants
© National Geographic

5. Atta leaf-cutter ants
© National Geographic

6. Atta leaf-cutter ants
© National Geographic

8. Oecophylla Weaver ants
© ameisenforum.de

9. © ameisenforum.de
Fourmis tisserandes

10. © ameisenforum.de
Oecophylla Weaver ants

11. © wynnie@flickr © forestryimages.org

12. Tofilski et al 2008
Forelius pusillus

13. Forelius pusillus hides the nest entrance at night
Tofilski et al 2008

14. Forelius pusillus hides the nest entrance at night
Tofilski et al 2008

15. Forelius pusillus hides the nest entrance at night
Tofilski et al 2008

16. Forelius pusillus hides the nest entrance at night
Tofilski et al 2008

17. Forelius pusillus hides the nest entrance at night
Avant
Workers staying outside die
« preventive self-sacrifice »
Tofilski et al 2008

18. Dorylus driver ants: ants with no home
© BBC

19. Animal biomass (Brazilian rainforest)
Mammals
Birds
Reptiles
Other insects Amphibians
from Fittkau & Klinge 1973
!
Earthworms
!
!
Spiders
Soil fauna excluding
earthworms,
ants & termites
Ants & termites

20. Genome Bioinformatics

21. This changes
454" everything.
Illumina"
Solid...
Any lab can
sequence
anything!

22. Big data is invading biology
• Genomics"
• Biodiversity assessments"
• Stool microbiome sequencing"
• Personalized medicine"
• Cancer genomics"
• Sensor networks - e.g tracking microclimates"
• Aerial surveys (Drones) - e.g. crop productivity; rainforest cover"
• Camera traps

25. Challenges
1. Getting up and running with Unix
(today)"
2. Algorithms in Bioinformatics: strengths & weaknesses
(Tuesday+Wednesday - Fabrizio Smeraldi)"
3. Bioinformatics databases
(Thursday to Monday - Ajanthah Sangaralingam / Chelala lab)"
4. DIY: genome assembly & identifying variants.
(Monday to Friday - Yannick)

26. Monday: "
Getting up and running with Unix
& High Performance Computing"
Because Excel just ain’t strong enough.
ITS Research Team (Lukasz Zalewski)"
1. Install virtualbox & biolinux. "
2. Introduction to Unix"
3. Using Apocrita HPC"
!

27. Algorithms for sequence alignment.
"Fabrizio Smeraldi - Algorithms for sequence alignment."
!
- dotplots- the concept of distance: Euclidean, hamming,
Levenshtein"
- dynamic programming and the Smith Waterman algorithm"
- local, global, semiglobal alignments"
- gap penalty models"
- basics of approximate methods (Blast)"
- scoring matrices (PAM, Blosum)"
- Profiles and PSI-Blast"
"" "
" "
" "

28. Databases for Bioinformatics !
!
- Biological databases & access to the annotated genomes
(lectures)"
- NCBI"
- Ensembl"
-UCSC"
- Entrez & Biomart"
- Genbank/Uniprot"
!
- Cancer resources and data portals "
- TCGA, ICGC and Cosmic (lecture and practical session)"""
" "
" "
"

29. Assembly & variant calling
• Genome assembly algorithms"
• Read mapping"
• Quality Assurance processes"
• Calling & visualising variants"
• Automated gene prediction"
• Doing things in the command-line