Tool to visualize microsyntenic regions

Question

[vharshavardhanan]

Hi dear friends

I want to generate microsytenic figure for my gene family. I have computed the microsyntenic regions for my gene family described in many articles eg: Jin et al. 2016, Chen et al. 2015. I have the data generated like

Region                                              Syntenic genes
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10340/POPTR_0003s13700   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10350/POPTR_0003s13710   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10370/POPTR_0003s13730   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10380/POPTR_0003s13740   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10390/POPTR_0003s13750   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10400/POPTR_0003s13760   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10410/POPTR_0003s13780   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10420/POPTR_0003s13790   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10460/POPTR_0003s13820   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10480/POPTR_0003s13830   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10490/POPTR_0003s13840
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10520/POPTR_0003s13880   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10530/POPTR_0003s13900   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10540/POPTR_0003s13910   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10550/POPTR_0003s13920   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10560/POPTR_0003s13940   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10590/POPTR_0003s13950   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10600/POPTR_0003s13960   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10610/POPTR_0003s13970   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10620/POPTR_0003s13980   
POPTR_0001s10490 - POPTR_0003s13840                 POPTR_0001s10630/POPTR_0003s13990

With this data I could like to create microsyntenic map similar to Figure3 presented in Jin et al. 2016 paper. However, I am not able to find any tool which gives me such output or any script too that can help me in generating this figure. Kindly need your guidance and help in sorting this out.

Any information from you will be greatly helpful

Thanks in advance

[Michael]

The article by Jin is paywalled, so you might need to sketch the graph. I am guessing that this plot is made by Circos, like the circular plot in Chin et al. That would be a good way of visualizing your data. However the data you show here are not sufficient, you need genomic coordinates to place the genes.

[vharshavardhanan]

Thank you michael. Try the paper here. I have the genomic information too for respective gene sets. I have used circos to compute whole genome syntenic regions, but for microsynteny there is a huge data (i have presented only a part in the question), visualization of those data in Circos will be very complicated for the readers to comprehend since my gene family is very large. Kindly look into Figure 5 in Chin et al, I could like to present my data in such a manner for very few gene sets. I could like to know which methods can be used to visualize my data. kindly help me.

[Michael]

Your link does not work, sorry

[vharshavardhanan]

Im sorry for the inconvience. But Figure 5 of Chen et al is similar to Figure 3 of Jin et al. So I guess you can refer figure 5 of Chen et al.