Question: how to analyze synteny between 4 genomes. please suggest suitable tool
1
gravatar for kaurjaimeet911
12 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 12 months ago by Kevin Blighe43k • written 12 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 12 months ago by microfuge1.1k

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

ADD REPLYlink written 12 months ago by Sej Modha4.2k
4
gravatar for jean.elbers
12 months ago by
jean.elbers1.1k
jean.elbers1.1k wrote:

https://github.com/rhysf/Synima

ADD COMMENTlink written 12 months ago by jean.elbers1.1k
1
gravatar for lieven.sterck
12 months ago by
lieven.sterck5.2k
VIB, Ghent, Belgium
lieven.sterck5.2k 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 12 months ago by lieven.sterck5.2k
1
gravatar for Kevin Blighe
12 months ago by
Kevin Blighe43k
Republic of Ireland
Kevin Blighe43k wrote:

You may find utility in these:

Kevin

ADD COMMENTlink written 12 months ago by Kevin Blighe43k
0
gravatar for jrj.healey
12 months ago by
jrj.healey12k
United Kingdom
jrj.healey12k 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 12 months ago by jrj.healey12k
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