SGP predictions combine geneid predictions with tblastx comparison of the Humangenome against the Mouse genome.

SGP was run on the unmasked fasta sequences for the following human genome version:

golden_path_20011222

It was also using homology evidences (the SRs - similarity regions) from TBLASTX, in which a masked version of the previous human genome assembly was comparedagainst the following mouse assembly version: (v3)

mmFeb2002 (MGSCv3)


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) 



NOTE: Coordinates of RefSeq genes were considered so that SGP(geneid) would not make any predictions in those regions.