How To Visualize Genomic Rearrangements And Synteny On A Larger Scale

Question

[biolab]

Dear All

I need to generate a graph for aligning a gene's structure in a couple of species. It is not sequence alignment, but a structure alingment, e.g. duplication, reversion etc, something like synteny anaylsis.

In fact, I am dealing with several hundred genes in ten species. So I need to run it in batch ranther than manually analyze these genes one by one. Could you please inform me how to achiev this analysis? THANK YOU VERY MUCH!

Answer 1

[Ashutosh Pandey]

http://www.cs.utah.edu/~miriah/mizbee/Overview.html

MizBee is a multiscale synteny browser for exploring conservation relationships in comparative genomics data. Using side-by-side linked views, MizBee enables efficient data browsing across a range of scales, from the genome to the gene. The design of MizBee is grounded in perceptual principles, and includes several techniques such as edge bundling and layering to enhance visual cues about conservation relationships related to proximity, size, similarity, and orientation.

I have never used it personally but have heard good things from my colleagues.

[biolab]

thanks a lot for your advices.