These SGP predictions combine geneid predictions with tblastx comparison of the Cow and Human genomes against the Chicken genome.  HSPs obtained from homologies of both species to G.gallus were combined

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

golden_path_200402 (Feb 2004)

SGP was also using homology evidences (the SRs - similarity regions) from TBLASTX, in which a masked version of the previous mouse genome assembly was compared against the following cow assembly version: 


goldenPath Cow genome assembly from Mar. 2005 (bosTau2) 
golden_path_200405 Human genome assembly from May 2004 (hg17)

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


chr1.sgp (geneid)

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) 


We have also included a "tgz" (tar-compressed file) containing all of the above.