problems with synteny - (Dec/26/2007 )

Hi all,

Has anyone done sequence analyses involving synteny? I have no idea how to even start on this. Many thanks to those who could help me out.

-blurtuna-

It depends which species you want to investigate. Although I don't have a lot of experience with it, there is an option in the Ensembl browser where you can ask for syntenic regions, and if you're interested in smaller regions, you can use the BLAT browser where you add a track with the conservation of your sequence in 12 (?) other organisms.

-dpo-

When some one does a synteny analysis, it usually means they have been analyzing the order of certain genes or genetic loci across many genomes. Well, Ensembl has an excellent browser to look out for synteny among many genomes.

Other than that if you explain specificially wat is ur aim (like wat genes u want to compare across wat genomes) then perhaps we can help.......

-string-

QUOTE (string @ Dec 28 2007, 04:18 AM)

Hi there,

I'm characterising a TNF receptor gene in zebrafish, and would like to find out if there is any syntenic relationship between zebrafish, xenopus, pufferfish, rat, mouse and human.

Thanks a lot for the advice. Will check out Ensembl for this.

Have a great weekend and a wonderful new year.

-blurtuna-