How to find Gene synteny among multiple sequences

Question

[Prasad]

Hi all,

I have to find the gene order (synteny) among two organism. The problem is I don't have draft genomes for any. For one organism I have ~17K scaffolds length ranging from (3MB to 500bp) and for another have ~18 super scaffolds (NCBI generated. each size > 13MB bp). I did the blast and tried to visualize in artemis-ACT tool. But it was very clumsy. Thought of circos plot, but I am not sure about it. How do I find the synteny when there are huge number of sequences and are there any better tools for visualization.

[Prasad]

Thanks for the replies. I will try both SyMap and Mauve.

Answer 1

[GouthamAtla]

You can try SyMap to construct synteny blocks. But it takes only 2500 sequences at max per query. So you may somehow reduce the number of scaffolds (concatenate them ) and load in to SyMap. It uses nucmer and promer internally to search for similar blocks.

Answer 2

[sentausa]

Have you tried Mauve?