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

SGP2 was run on the masked fasta sequences for the rat genome assembly rn6 (made up of 883 genomics sequences including 22 chromosomes), and generated 37,981 gene predictions.

SGP2 uses homology evidences (the SRs - similarity regions) from TBLASTX, in which a masked version of the rn6 genome assembly was compared against the hg38 human genome assembly.

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

rn6.sgp2

rn6.sgp2.gff

rn6.sgp2.gff3

rn6.sgp2.gtf

rn6.sgp2.cds (nucleotide sequence of predicted sequences)

rn6.prot (amino acid sequence of predicted protein sequences)