1.           Sequence Analysis with Artemis and Artemis Comparison Tool (ACT) Carribean Bioinformatics Workshop 18 th -29 th January, 2010

2. ICGEB Bioinformatics Workshop Introduction to Artemis Comparison T ool (ACT)

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

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

5. ACT- Artemis Comparison Tool

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

7. Region of Synteny Genome 1 Genome 2

8. Looking for ‘pseudogenes’ Genome 1 Genome 2

9. Rearrangements Genome 1 Genome 2

10. Insertion or deletion Genome 1 Genome 2

11. Paralogous gene family expansions Genome 1 Genome 2

12. ACT Prokaryotic examples

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

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

15. Burkholderia pseudomallei vs Burkholderia mallei

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

17. Mu50 N315 MRSA252 MW2 MSSA476 Multiple genomes

18. Pathogenicity islands/prophages sopEVi antigentype IV pilus tRNA-Phe S. typhi E. coli

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

20. Small rearrangements

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

22. ACT Eukaryotic examples

23. Viewing Annotation in Artemis: P. chabaudi AS & P. falciparum 3D7 Viewing Annotation in ACT: P. chabaudi AS vs P. falciparum 3D7

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

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

26. Pseudogenes P. chabaudi AS P. falciparum 3D7

27. Generating ACT comparison files using WebACT

28. ACT comparison files (‘crunch’ files) ACT supports three different comparison file formats: 1) BLAST version 2.2.2 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. 1399 97.00 940 2539 sequence1.dna 1 1596 AF140550.seq 1033 93.00 9041 10501 sequence1.dna 9420 10880 AF140550.seq 828 95.00 6823 7890 sequence1.dna 7211 8276 AF140550.seq 773 94.00 2837 3841 sequence1.dna 2338 3342 AF140550.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.

29. Basic features of Artemis Comparison Tool (ACT)