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The Artemis Comparison Tool
ACT
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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
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Region sharing similarity
Representing sequence similarity/identity MQALL… …RHP Region sharing similarity (BlastP) MAVV… …RHP
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ACT- Artemis Comparison Tool
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Orthologue of E. coli b0170 Orthologue of E. coli b0169 Orthologue of E. coli b0171
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Genome 1 Genome 2 Region of Synteny
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Genome 1 Genome 2 Rearrangements
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Genome 1 Genome 2 Insertion or deletion
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Whole genomes Chromosomal rearrangements Pathogenicity islands/prophages Gene acquisition and loss Gene rearrangements Pseudogenes Phase variation Single nucleotides
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Prokaryotic examples
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Whole genomes: S. typhi vs. E. coli
SPI-2 SPI-9 SPI-1 SPI-10 SPI-7 Vi S. typhi DNA matches E. coli
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Multiple genomes B. pertussis IS elements B. bronchiseptica prophage
B. parapertussis IS elements
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Whole genomes: S. aureus Mu50 vs. N315
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Multiple genomes Mu50 N315 MRSA252 MW2 MSSA476
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Pathogenicity islands/prophages
tRNA-Phe type IV pilus sopE Vi antigen S. typhi E. coli
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Gene acquisition and loss
Insect toxin Y. pestis Y. enterocolitica
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Small rearrangements
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Pseudogenes secreted effector protein (type-III) S. typhi
S. typhimurium
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ACT Eukaryotic examples
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Synteny:T.annulata and T. parva (Chr2)
BlastN & TBlastX T. annulata T. parva
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Synteny: TA & TP ACT comparison
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T. annulata & T. parva comparison (Chr 3)
Synteny Genus-specific expansion Species-specific expansion Species-specific genes
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P. falciparum vs P. knowlesi: break in synteny
Chrl3 P. knowlesi
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Improving gene prediction with ACT
P. falciparum chr13 P. knowlesi Comparison between orthologous genes in P. falciparum and P. knowlesi
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ACT comparison: 3 malaria species
P. yoelii P. falciparum P. knowlesi
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“species-specific” genes at interruptuions in synteny
Plasmodium falciparum Plasmodium knowlesi Plasmodium yoelii
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ACT comparison of qut gene cluster
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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.
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