We would like to use GBrowse_syn to display syntenic regions resulting from a whole genome duplication within the same species. GBrowse_syn currently disallows the use of the same species in both the species1 and species2 columns of the "alignment" table; e.g., part of the input file to gbrowse_syn_load_alignment_database.pl looks like this:
glycine_max Gm01 170877 269340 - . glycine_max Gm08 46288465 46349001 - .
glycine_max Gm01 275574 683275 - . glycine_max Gm07 14801336 15414305 - .
I was able to work around this with the attached one-line change to gbrowse_syn. Note that I'm not aware of the ramifications this change would have with a multi-species configuration, as I didn't test it in that situation. If this fix isn't desirable for some reason, suggestions on other ways to work around this issue would be appreciated.
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