Question

How to find synteny between genes and Chromosomes?

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10.0 years ago

vharshavardhanan ▴ 30

Hi, I want to find the syntenic regions between my genes (300-1200bp) and correspondaing genome. I used SynMap to find the syntenic regions but unfortunately I am not getting any graphical map but I am getting the tabular form result showing my syntenic regions (position and chromosome). Any idea why I am not able to view graphical map of my result?

Genes SynMap Chromosome Synteny • 4.3k views

ADD COMMENT • link updated 2.7 years ago by Ram 44k • written 10.0 years ago by vharshavardhanan ▴ 30

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Post the error that you are getting.

ADD REPLY • link updated 2.7 years ago by Ram 44k • written 10.0 years ago by GouthamAtla 12k

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'No syntenic blocks founded' - is the error which appear everytime when I perform in Synmap.

ADD REPLY • link 10.0 years ago by vharshavardhanan ▴ 30

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Why do you think it's an error? There may be no synteny blocks. A synteny block is not a simple match. You need to configure properly what is a synteny block in symap.

ADD REPLY • link updated 2.7 years ago by Ram 44k • written 10.0 years ago by GouthamAtla 12k

Ram · Answer 1 · 2014-11-26

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10.0 years ago

Denise CS ★ 5.2k

I don't use SynMap but synteny maps and data are available in Ensembl. Not sure which species you are interested in but this is a nice image you can get.

ADD COMMENT • link updated 2.7 years ago by Ram 44k • written 10.0 years ago by Denise CS ★ 5.2k

score 0 · Answer 2 · 2014-11-26

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10.0 years ago

vharshavardhanan ▴ 30

Only draft genome is available for my species so I think I cant use Ensembl for synteny mapping. If you know how to find synteny between genes and chromosomes in offline software or online tool kindly let me know.

ADD COMMENT • link 10.0 years ago by vharshavardhanan ▴ 30