My master's thesis on SyMAP, a synteny mapping and analysis program.

1. SyMAP Synteny Mapping and Analysis Program Austin Shoemaker

5. Genome Rearrangements Rearrangement Scenario Result Inversion Duplication Insertion Deletion A BCD E A DCB E A B C AC AB A C B A B CD A B B CD A B C A B C B , A BB C AB AB AB

18. Component Summary

19. Finding Chains

23. FPC Synteny Properties 1 x 2 o 3 x 4 x 5 o 6 8 # x 9 x a x b x c x 7 x 1 2 3 4 5 6 7 8 9 a b c Genome A (FPC map) Genome B (sequenced genome)

24. Noise

37. All Blocks ↔ Sequenced Chromosomes

38. Blocks ↔ Sequenced Chromosome

39. Genome ↔ Genome Dot Plot

40. Chromosome ↔ Chromosome Dot Plot

41. Block ↔ Sequenced Chromosome

42. Subset Flipped

43. Contig ↔ Sequenced Chromosome

44. Filters and Controls

45. FPC ↔ Sequenced Chromosome ↔ FPC

46. FPC ↔ FPC

47. Close-up of Gene