These SGP predictions combine geneid predictions with tblastx comparison of the Human Genome against the Rat genome.

SGP was run on the masked fasta sequences for the following rat genome version:

rnNov2004 (rn4)

It used homology evidences (the SRs - similarity regions) from TBLASTX, in which a masked version of the previous rat genome assembly was compared against the following human assembly version: 


golden_path_200603 (from ncbi Human Genome hg18) 


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


chr1.sgp

chr1.gff

chr1.gtf

chr1.cds (nucleotide sequence of predicted sequences)

chr1.prot (amino acid sequence of predicted protein sequences)

chr1_tbxsr.gff (gff output of geneid combined with tblastx)