tools for synteny analysis

… 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???

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

… my experience LAF2 LAF13 human

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

… 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

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

… 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

… 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

… blast & excel John Bowers

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

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

… vitis/tomato in SyMap

… “blocks only” in SyMap

filtering in SyMap tomato chr.1 vs. vitis

lettuce LG7 vs. vitis

… 2D plot in Symap lettuce LG7 vs. vitis

… 3D plot in Symap

… McScan http://chibba.pgml.uga.edu/duplication/mcscan/ microsynteny calculation and visualization lettuce/potato comparison (BGI)

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

… GBrowse_syn (distantly related species?)

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 ?

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

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

Genomicus webserver for animal synteny gene level comprehensive summarizes clade characteristics

compositaezome.phytozome.net

… phytozome micro-synteny

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

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

Cinteny - gene level plots

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

Cinteny: whole genome cpomparisons

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

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

… Vistapoint dot plots published genome sequences

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

… whole genome dot plots

… ks histogram in CoGe

… custom analysis in CoGe choice of alignment algorithms, …

… custom analysis in CoGe it may take a few hours

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 ?

OSLAY synthesis of two incomplete assemblies of related species

… syntenic path assembly option in CoGe SynMap

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

… 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