Question: how to analyze synteny between 4 genomes. please suggest suitable tool
1
gravatar for kaurjaimeet911
6 weeks 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 26 days ago by Kevin Blighe24k • written 6 weeks ago by kaurjaimeet91110

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

ADD REPLYlink written 6 weeks ago by microfuge910

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

ADD REPLYlink written 26 days ago by Sej Modha3.1k
4
gravatar for jean.elbers
6 weeks ago by
jean.elbers290
jean.elbers290 wrote:

https://github.com/rhysf/Synima

ADD COMMENTlink written 6 weeks ago by jean.elbers290
1
gravatar for lieven.sterck
26 days ago by
lieven.sterck1.9k
Belgium, Ghent, VIB
lieven.sterck1.9k 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 26 days ago by lieven.sterck1.9k
1
gravatar for Kevin Blighe
26 days ago by
Kevin Blighe24k
Republic of Ireland
Kevin Blighe24k wrote:

You may find utility in these:

Kevin

ADD COMMENTlink written 26 days ago by Kevin Blighe24k
0
gravatar for jrj.healey
6 weeks ago by
jrj.healey4.8k
United Kingdom
jrj.healey4.8k 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 6 weeks ago by jrj.healey4.8k
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