[maker-devel] RepeatMasker masking olfactory receptors

[Annabel Beichman]

Hi Carson,
I have a question about RepeatMasker within Maker —
I am finding that all class II olfactory receptors (families like OR2, OR5) are being masked by RepeatMasker as “RTE-BovB” repeats. This leads to them not being annotated by Maker. I don’t expect my species (a mustelid) to have a large number of Bov-B repeats, and when I put the sequences annotated in my genome as RTE-BovB into repbase’s CENSOR only 13 out of 960 sequences have a hit to anything in repbase. If I put those same sequences into NCBI blast, however, they all blast to olfactory receptors. I am finding the same pattern with another related mustelid de novo genome, and took the Ensembl ferret genome and ran it through the same pipeline and am finding a large number of Bov-B repeats there as well, despite there being none in the official annotation of that genome. 

I used RepeatMasker with all species libraries, plus a custom library from RepeatModeler.

Any idea what might be going on? 

Thanks so much!

~ Annabel