Hi all,
I want to find orthologous regions between Medicago truncatula and Arabidopsis thaliana. Or to convert the coordinates from one species to another.
I found that liftover can convert the coordinates between assemblies. But I'm afraid that it is not suitable for converting coordinates from Ath. to Mtr. Because there are 5 chromosomes in Ath. but there are 8 chrs in Mtr, I don't know how liftover can deal with this issue and there is no chain files for Ath. or Mtr. (I have not used liftover yet.)
So I may need to find the orthologous regions (including genes and non coding regions) instead. Is there any tool for locating orthologous regions between two species? And is there any database that I can download the ortholog genes between Ath. and Mtr?
Thanks!
Xiaohui
I want to find orthologous regions between Medicago truncatula and Arabidopsis thaliana. Or to convert the coordinates from one species to another.
I found that liftover can convert the coordinates between assemblies. But I'm afraid that it is not suitable for converting coordinates from Ath. to Mtr. Because there are 5 chromosomes in Ath. but there are 8 chrs in Mtr, I don't know how liftover can deal with this issue and there is no chain files for Ath. or Mtr. (I have not used liftover yet.)
So I may need to find the orthologous regions (including genes and non coding regions) instead. Is there any tool for locating orthologous regions between two species? And is there any database that I can download the ortholog genes between Ath. and Mtr?
Thanks!
Xiaohui
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