Question: How to find Gene synteny among multiple sequences
0
gravatar for Prasad
4.3 years ago by
Prasad1.5k
India
Prasad1.5k wrote:

Hi all,

I have to find the gene order (synteny) among two organism. The problem is i dont 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.

tool order gene • 2.0k views
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Prasad1.5k

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. 

ADD REPLYlink written 4.3 years ago by geek_y9.3k
0
gravatar for sentausa
4.3 years ago by
sentausa630
France
sentausa630 wrote:

Have you tried Mauve?

ADD COMMENTlink written 4.3 years ago by sentausa630
0
gravatar for Prasad
4.3 years ago by
Prasad1.5k
India
Prasad1.5k wrote:

thanks for the reply. i will try both SyMap and Mauve. 

ADD COMMENTlink written 4.3 years ago by Prasad1.5k
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