Ortholog Map from Whole Genome Alignment (WGA)

Question

[Felix Bemm]

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.

Answer 1

[Felix Bemm]

Answer

1. maf2hal
2. gff2gtf
3. homGeneMapping (http://manpages.ubuntu.com/manpages/zesty/man1/homGeneMapping.1.html)