Our SGP2 (http://genome.crg.es/software/sgp2/index.html) predictions on the cow genome combine geneid predictions with tblastx comparison of the human genome against the cow genome.

SGP2 was run on the masked fasta sequences for the cow genome assembly bosTau8 (made up of 3179 genomics sequences including 30 chromosomes), and generated 35,519 gene predictions.

SGP2 uses homology evidences (the SRs - similarity regions) from TBLASTX, in which a masked version of the bosTau8 genome assembly was compared against the hg38 human genome assembly.

Predictions were obtained per chromosome and output in the following formats:

bosTau8.Hs-Mm.sgp2

bosTau8.Hs-Mm.sgp2.gff

bosTau8.Hs-Mm.sgp2.gff3

bosTau8.Hs-Mm.sgp2.gtf

bosTau8.Hs-Mm.sgp2.cds (nucleotide sequence of predicted sequences)

bosTau8.Hs-Mm.prot (amino acid sequence of predicted protein sequences)