How to find synteny between genes and Chromosomes?

Question

[vharshavardhanan]

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?

[GouthamAtla]

Post the error that you are getting.

[vharshavardhanan]

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

[GouthamAtla]

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.

Answer 1

[Denise CS]

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.

Answer 2

[vharshavardhanan]

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.