These SGP predictions combine geneid predictions with tblastx comparison of the Cow Genome against the Chicken genome.

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

golden_path_200402 (Feb 2004)

It 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) 


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) 


