Question

how to analyze synteny between 4 genomes. please suggest suitable tool

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6.5 years ago

kaurjaimeet911 ▴ 10

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

RNA-Seq sequencing next-gen Assembly • 5.2k views

ADD COMMENT • link updated 6.4 years ago by Kevin Blighe 88k • written 6.5 years ago by kaurjaimeet911 ▴ 10

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

ADD REPLY • link 6.5 years ago by microfuge ★ 1.9k

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

ADD REPLY • link 6.4 years ago by Sej Modha 5.3k

score 4 · Answer 1 · 2018-06-04

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6.5 years ago

jean.elbers ★ 1.7k

https://github.com/rhysf/Synima

ADD COMMENT • link 6.5 years ago by jean.elbers ★ 1.7k

score 1 · Answer 2 · 2018-06-21

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6.4 years ago

lieven.sterck 15k

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 COMMENT • link 6.4 years ago by lieven.sterck 15k

score 1 · Answer 3 · 2018-06-21

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6.4 years ago

Kevin Blighe 88k

You may find utility in these:

Synteny Portal: a web-based application portal for synteny block analysis
mySyntenyPortal: an application package to construct websites for synteny block analysis (just published)
Genomicus (recommended by a colleague)

Kevin

ADD COMMENT • link 6.4 years ago by Kevin Blighe 88k

score 0 · Answer 4 · 2018-06-04

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6.5 years ago

Joe 21k

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 COMMENT • link 6.5 years ago by Joe 21k