Entering edit mode
7.0 years ago
Felix Bemm
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20
Challenge
Take a multiple whole genome alignment (MAF or fasta) and associated genome annotations (GFF) and generate a ortholog/paralog map. To keep it simple, overlapping annotations would qualify as paralog/ortholog if they cover each other reasonably well in the WGA (e.g. 75% sequence overlap).
Examples
Mugsy-annotator would work for bacterial genomes but not for larger Eukaryota (at least not for the data that I have).
Question
Is there an elegant solution already around or is that something I would need to develop by myself?
Ideas are very much appreciated.