Question: how to analyze synteny between 4 genomes. please suggest suitable tool
1
gravatar for kaurjaimeet911
5 months ago by
kaurjaimeet91110 wrote:

i want to analyze synteny of 4 genomes .therefore it is my humble request to kindly suggest any suitable tool

ADD COMMENTlink modified 4 months ago by Kevin Blighe32k • written 5 months ago by kaurjaimeet91110

Synmap is a good tool but works only up to 3 genomes (https://genomevolution.org/coge/SynMap3D.pl)

ADD REPLYlink written 5 months ago by microfuge950

+1 for Synima, I have recently used to for multiple Plasmodium genomes and it worked like a charm!

ADD REPLYlink written 4 months ago by Sej Modha3.8k
4
gravatar for jean.elbers
5 months ago by
jean.elbers450
jean.elbers450 wrote:

https://github.com/rhysf/Synima

ADD COMMENTlink written 5 months ago by jean.elbers450
1
gravatar for lieven.sterck
4 months ago by
lieven.sterck3.1k
VIB, Ghent, Belgium
lieven.sterck3.1k wrote:

i-ADHoRe is another option, rather for analyzing (or looking for synteny) then visualising though (can't make up from your question what the exact goal is?)

ADD COMMENTlink written 4 months ago by lieven.sterck3.1k
1
gravatar for Kevin Blighe
4 months ago by
Kevin Blighe32k
Republic of Ireland
Kevin Blighe32k wrote:

You may find utility in these:

Kevin

ADD COMMENTlink written 4 months ago by Kevin Blighe32k
0
gravatar for jrj.healey
5 months ago by
jrj.healey8.6k
United Kingdom
jrj.healey8.6k wrote:

I suggest Sibelia. It will draw you a circos plot of the synteny conservation. If you're only interested in specific gene regions/operons, try MultiGeneBlast.

ADD COMMENTlink written 5 months ago by jrj.healey8.6k
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