[maker-devel] Annotations from proteins, follow-up

[Marc Höppner]

Hi,

I had previously inquired about protein-based gene building (for example to create a training set for SNAP). This is currently possible with Maker (2.31), but I noticed a limitation. Specifically, I tend to run Maker once to generate all the raw computes (protein and set alignments, mostly). I then separate these out into GFF files that I can store away and use in various combinations of settings and data in parallel. 

However, the protein2genome option does not seem to work off pre-aligned protein data (e.g. protein2genome.gff produced with Maker). Is that intentional and is there a work-around? Or is the only option to run this with fasta files?

Cheers,

Marc


Marc P. Hoeppner, PhD

Department for Medical Biochemistry and Microbiology
Uppsala University, Sweden
marc.hoeppner at imbim.uu.se