1. tools for synteny analysis

2. … synteny "on the same ribbon"
sensu stricto - no gene order information collinearity – recognizable (imperfect) synteny <-> conserved synteny syntenic chromosomes, syntenic blocks, perfect ~ imperfect synteny, thresholds???

3. … outline
scales of synteny why care about synteny? categories of tools examples recommendations

4. … my experience
LAF2
LAF13
human

6. … why bother?
aid genome assembly and annotation through alignments of orthologous regions
study large-scale rearrangements
trace genome evolution
identify functional elements (enhancers, …)

7. … orders of magnitude
macrosynteny whole genome translocations, fusions, … reducing complexity graphically coarse, neglecting smaller imperfections ? microsynteny gene level homology visualizations domain-, exon-alignments alignments of multiple species

8. … excellent tools
standalone <-> web services more than 20 software packages 5 or more web based tools (3 run user data: GSV, AutoGraph, Cinteny)

9. … tools BLASTZ, LAST, MULTIZ, Shuffle-LAGAN
all-in-one <-> requiring prior alignments
all-in-one solutions:
Mauve (Aaron Darling)
Symap
CoGe syn (for published genomes)
prior alignments:
BLASTZ, LAST, MULTIZ, Shuffle-LAGAN

10. … categories
micro & macro synteny: Mizbee, Symap, Cinteny, CoGe Synmap, Sybil, … micro synteny: Synbrowse, GBrowse_syn, SynView, GSV, AutoGraph, Phytozome, Vistapoint, … interactive dot plot: GenoPix 2D Plotter assembly tools: Oslay, CoGe Syn

11. … blast & excel
John Bowers

13. … MizBee (cs.utah.edu/~miriah/mizbee)
integrated and interactive synteny visualization on three scales
documentation on setup is missing

14. … SyMap agcol.arizona.edu/software/symap all-in-one solution dot-plots
2D and 3D synteny plots
interactive filtering

15. … vitis/tomato in SyMap

16. … “blocks only” in SyMap

18. filtering in SyMap
tomato chr.1 vs. vitis

19. lettuce LG7 vs. vitis

20. … 2D plot in Symap
lettuce LG7 vs. vitis

21. … 3D plot in Symap

22. … McScan
microsynteny calculation and visualization lettuce/potato comparison (BGI)

23. Gbrowse related synteny viewer
Synbrowse synbrowse.org SynView gmod.org/wiki/SynView works in GBrowse GBrowse_syn gmod.org/wiki/GBrowse_syn still developed

24. … GBrowse_syn (distantly related species?)

25. Genome Synteny Viewer
cas-bioinfo.cas.unt.edu/gsv/homepage.php - webservice and standalone download for micro-synteny - excellent video tutorials - works only with small datasets ?

26. GENOMICUS http://www.dyogen.ens.fr/genomicus
for beasts only

27. GENOMICUS http://www.dyogen.ens.fr/genomicus

28. Genomicus webserver for animal synteny gene level comprehensive
summarizes clade characteristics

29. compositaezome.phytozome.net

30. … phytozome micro-synteny

31. atgc.org/GenoPix_2D_Plotter
GenoPix 2D Plotter interactive Alex Kozik

32. … Cinteny
cinteny.cchmc.org: - webservice - simple file format - whole genome to gene level scale - adjustable syteny block thresholds

33. Cinteny - gene level plots

34. Cinteny: - variation due to gap length and min. length parameters

35. Cinteny: whole genome cpomparisons

36. AutoGraph
autograph.genouest.org generates high resolution synteny maps calculates synteny blocks (threshold options) and numbers of rearrangements

37. … Vistapoint
LBNL/JGI group genome.lbl.gov/vista
microsynteny only

38. … Vistapoint dot plots
published genome sequences

39. … CoGe synteny tools
synteny.cnr.berkeley.edu/CoGe CONs: - no circle plots (humor alert) - it is complex PROs: - this is a treasure chest !!!

40. … whole genome dot plots

41. … ks histogram in CoGe

42. … custom analysis in CoGe
choice of alignment algorithms, …

43. … custom analysis in CoGe
it may take a few hours

44. OSLAY http://ab.inf.uni-tuebingen.de/software/oslay/
ordering of conserved blocks according to synteny synthesis of incomplete assemblies of related species bacterial genomes only ?

45. OSLAY
synthesis of two incomplete assemblies of related species

46. … syntenic path assembly option in CoGe SynMap

47. … our lettuce data Symap (vitis, tomato) Cynteny
Blast/Excel method sunflower, lettuce/lettuce
improve pseudomolecules ?

48. … preliminary recommendations
comparing published plant genomes:
- explore CoGe’s tools
pre-publication data analysis:
- Symap and Mizbee have lots of tempting features,
but John’s Excel tabulation works
should have tried MacScan
hosting own genome browser:
- Gbrowse-Syn