Synteny analysis

[fanwei]

Dear all,

Have you ever been involved in synteny analysis? I feel confused about that.
Can i just input a gene sequence to compare synteny? Or I must input the genomic sequence?
And how do you implement synteny analysis ? Can you recommend me some easy ways?

Thank you!

[SNPsaurus]

You might look at this paper, particularly the comparative genomics methods section:

http://www.genetics.org/content/188/4/799.full

[fanwei]

You might look at this paper, particularly the comparative genomics methods section:
http://www.genetics.org/content/188/4/799.full

Have you ever done this analysis before? I feel confused.
I want to analyze synteny of a targeted gene between two species. But one of them just has some scaffold sequences (unfinished sequencing).Can it be used to analyze?

Thank you!

[jimmybee]

Have you ever done this analysis before? I feel confused.
I want to analyze synteny of a targeted gene between two species. But one of them just has some scaffold sequences (unfinished sequencing).Can it be used to analyze?

Thank you!

Are you looking to just analyse one gene or a gene family? If its one gene then it should be a simple BLAST against scaffold sequences to identify it. If these are unplaced scaffolds that have no chromosome or genotyping information then you're not going to gauge synteny.

[fanwei]

Are you looking to just analyse one gene or a gene family? If its one gene then it should be a simple BLAST against scaffold sequences to identify it. If these are unplaced scaffolds that have no chromosome or genotyping information then you're not going to gauge synteny.

I know! Thank you very much!