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Sequence Analysis with Artemis and Artemis Comparison Tool (ACT) Carribean Bioinformatics Workshop

Sequence Analysis with Artemis and Artemis Comparison Tool (ACT) Carribean Bioinformatics Workshop 18 th -29 th January, 2010. Sequence Analysis with Artemis and Artemis Comparison Tool (ACT) Carribean Bioinformatics Workshop 18 th -29 th January, 2010. Whole genomes.

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Sequence Analysis with Artemis and Artemis Comparison Tool (ACT) Carribean Bioinformatics Workshop

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  1. Sequence Analysis with Artemis and Artemis Comparison Tool (ACT) Carribean Bioinformatics Workshop 18th-29th January, 2010 Sequence Analysis with Artemis and Artemis Comparison Tool (ACT) Carribean Bioinformatics Workshop 18th-29th January, 2010

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

  3. 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 Looking for ‘pseudogenes’

  8. Genome 1 Genome 2 Rearrangements

  9. Genome 1 Genome 2 Insertion or deletion

  10. Genome 1 Genome 2 Paralogous gene family expansions

  11. ACTProkaryotic examples

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

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

  14. Burkholderia pseudomallei vs Burkholderia mallei

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

  16. Mu50 N315 MRSA252 MSSA476 MW2 Multiple genomes

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

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

  19. Small rearrangements

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

  21. ACTEukaryotic examples

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

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

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

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

  26. Generating ACT comparison files using WebACT

  27. 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.

  28. Basic features of Artemis Comparison Tool (ACT) Live demo!

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