Entering edit mode
23 months ago
If I have 2 strain of same species. And I have genomic island regions on excel sheet. And now I want to view the synteny of those regions on both strain. How can I do this?
I have used a tool names synvisio there a collinearity file and gff file and track file they use as input. If I can view synteny by this tool, how can I download collinearity file and gff file for the genetic island region for 2 different strain.
To my knowledge there are two types of synteny tools: anchored and alignment based (not official names, just my naming convention).
Anchored uses features such as genes that are shared among species to investigate synteny around these features. Alignment breaks genomes into kmers and aligns them to each other. It's hard to see which is better for you without more information about the genomic islands, but I would probably go for alignment tools. Once the analysis is complete, just overlap your genomic islands with the synteny output files.
I use
Satsuma2[REF], which works well and pairs nicely with Circos for visualisation. I would then colour only lines from within the genomic islands.GFF files should be available on any online database that has an assembly of the model system you are using (i.e., NCBI, Ensembl, Vectorbase, Flybase, etc...).