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
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
17
18
… 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
- it is complex
(humor alert)
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