1. The Artemis Comparison Tool
ACT

2. Comparative Genomics
It might be expected that if two organisms diverged from a common ancestor, they should share:
- similar gene content
- similar gene organization
However, genome evolution is a highly dynamic process:
- gene acquisition and gene loss will change genome content
- gene rearrangements will change the order of genes.
Comparative genomics tell us about common and unique features between different organisms at the genome level.
Identification of similarities and differences between genomes may allow us to understand:
- How two organisms evolved
- Why certain organisms cause diseases while others do not

3. Region sharing similarity
Representing sequence similarity/identity
MQALL…
…RHP
Region sharing similarity
(BlastP)
MAVV…
…RHP

4. ACT- Artemis Comparison Tool

5. Orthologue of E. coli b0170
Orthologue of E. coli b0169
Orthologue of E. coli b0171

6. Genome 1
Genome 2
Region of Synteny

7. Genome 1
Genome 2
Rearrangements

8. Genome 1
Genome 2
Insertion or deletion

9. Whole genomes
Chromosomal rearrangements
Pathogenicity islands/prophages
Gene acquisition and loss
Gene rearrangements
Pseudogenes
Phase variation
Single nucleotides

10. Prokaryotic examples

11. Whole genomes: S. typhi vs. E. coli
SPI-2
SPI-9
SPI-1
SPI-10
SPI-7 Vi
S. typhi
DNA
matches
E. coli

12. Multiple genomes B. pertussis IS elements B. bronchiseptica prophage
B. parapertussis
IS elements

13. Whole genomes: S. aureus Mu50 vs. N315

14. Multiple genomes
Mu50
N315
MRSA252
MW2
MSSA476

15. Pathogenicity islands/prophages
tRNA-Phe
type IV pilus
sopE
Vi antigen
S. typhi
E. coli

16. Gene acquisition and loss
Insect toxin
Y. pestis
Y. enterocolitica

17. Small rearrangements

18. Pseudogenes secreted effector protein (type-III) S. typhi
S. typhimurium

19. ACT Eukaryotic examples

20. Synteny:T.annulata and T. parva (Chr2)
BlastN & TBlastX
T. annulata
T. parva

21. Synteny: TA & TP ACT comparison

22. T. annulata & T. parva comparison (Chr 3)
Synteny
Genus-specific expansion
Species-specific expansion
Species-specific genes

23. P. falciparum vs P. knowlesi: break in synteny
Chrl3
P. knowlesi

24. Improving gene prediction with ACT
P. falciparum
chr13
P. knowlesi
Comparison between orthologous genes in P. falciparum and P. knowlesi

25. ACT comparison: 3 malaria species
P. yoelii
P. falciparum
P. knowlesi

26. “species-specific” genes at interruptuions in synteny
Plasmodium falciparum
Plasmodium knowlesi
Plasmodium yoelii

27. ACT comparison of qut gene cluster

28. Generating ACT comparison files
ACT supports three different comparison file formats:
1) BLAST version output: The blastall command must be run with
the -m 8 flag which generates one line of information per HSP.
2) MEGABLAST output: ACT can also read the output of MEGABLAST,
which is part of the NCBI blast distribution.
3) MSPcrunch output: MSPcrunch is program for UNIX and GNU/Linux
systems which can post-process BLAST version 1 output into an
easier to read format. ACT can only read MSPcrunch output with
the -d flag.
Here is an example of an ACT readable comparison file generated by MSPcrunch -d.
sequence1.dna AF seq
sequence1.dna AF seq
sequence1.dna AF seq
sequence1.dna AF seq
The columns have the following meanings (in order): score, percent
identity, match start in the query sequence, match end in the query
sequence, query sequence name, subject sequence start, subject sequence
end, subject sequence name.
The columns should be separated by single spaces.