Tyler phringe fri 1120

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Tyler phringe fri 1120

  1. 1. PHRINGE Synteny tool http://oomycetes.genomeprojectsolutions-databases.com/ [top half of home page]
  2. 2. PhiGS Synteny tool http://oomycetes.genomeprojectsolutions-databases.com/ [top half of home page] Entry to browser
  3. 3. source species for display gaps in synteny pixels for display target species Units are gene models not sequence length colored models have orthologs grey models have no orthologs Models are color coded by matching scaffold
  4. 4. End position setting controls how many gene models are packed into the display window
  5. 5. Mouse-over scaffold name gives pop-up of scaffold info
  6. 6. Mouse-over gene model gives pop-up of brief gene model info Click on gene model links to detailed gene model info Hint: if the gene model bars are too narrow to do this easily, zoom in
  7. 7. Scaffold and coordinates Protein ID PhiGs gene number Clickable link to source database
  8. 8. List of hits in source species and several target species Hits link to databases
  9. 9. P.sojae and P. ramorum preserve gene order except in the vicinity of virulence genes 14 Avr1b
  10. 10. 188 100 Avh72 Avh277 (sc 1079) Use of the synteny map to track down Avr1a
  11. 11. Synteny among oomycete genomes a very few RXLR effectors are syntenic Ps v1 Sc55 Pi v1 contig1.1 Ha v6 Sc9 Pr v1 Sc1 Pr v1 Sc104 100 149 368 14 683 737 Ps v1 Sc137 26 1 1 32 HaRxL23 PrAvh388 PsAvh73 PiRxLRdEER_192

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