Entering edit mode
9 months ago
I0110
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140
Hi all,
Is there any tools that can be used for identifying syntenic gene pairs? I want to use the latest annotation of Arabidopsis and tomato to find syntenic gene pairs. I checked out some web tools such as SynMap, but it appears that I cannot upload new annotation for the analysis. Thanks!
Just for clarity, are these genes pairs required to be in the same genomic region in both genomes? Or are they just meant to be orthologous (i.e, high sequence similarity and putatively evolved from the same ancestral gene)? I see these terms used interchangeably, so want to be clear.
If the former, then there are a few anchored synteny tools that could be suitable, benchmarking study here.
If the latter, tools like OrthoMCL and OrthoFinder are great.
I want to find those gene pairs in the same genomic region. It seems to be difficult to do!
Then you have the anchored synteny tools as indicated in my previous message. MCScanX seems like it would fit your requirements well, and then you'd just have to come up with a reasonable set of filtering parameters to identify your candidate gene pairs.