Gene fusions/duplications in GRIMM-Synteny?
I am attempting to look at homologous synteny blocks in an organelle genome across a few different species using GRIMM Synteny.
Reading the documentation files and Tessler & Bourque (2008), I have understood how to manually code sequence data to a format that GRIMM Synteny can accept (I am using gene coordinates):
1 1 start_1 length_1 strand_1 1 start_2 length_2 strand_2 etc.
This works great for most of the genes I am looking at. However, I seem to have gotten stuck in two particular situations: gene fusions and gene duplications (and since it is an organelle, it is a unichromosomal analysis). The typical situation here is that one species has a gene fusion or gene duplication, but another one in the analysis does not.
Can those genes be used in GRIMM Synteny? If so, in what format should they be written?
I have performed a forum search, a Google search and a search at Pubmed without any luck so far.
Thank you for your time, have a nice day.
Reading the documentation files and Tessler & Bourque (2008), I have understood how to manually code sequence data to a format that GRIMM Synteny can accept (I am using gene coordinates):
1 1 start_1 length_1 strand_1 1 start_2 length_2 strand_2 etc.
This works great for most of the genes I am looking at. However, I seem to have gotten stuck in two particular situations: gene fusions and gene duplications (and since it is an organelle, it is a unichromosomal analysis). The typical situation here is that one species has a gene fusion or gene duplication, but another one in the analysis does not.
Can those genes be used in GRIMM Synteny? If so, in what format should they be written?
I have performed a forum search, a Google search and a search at Pubmed without any luck so far.
Thank you for your time, have a nice day.