This track contains tBLASTn alignments of the peptides from the predicted and known genes identified in the hg16 Known Genes track as of 27 May 2004.
First the predicted proteins from the human Known Genes track were aligned with the human genome using the blat program to discover exon boundaries. Next the amino acid sequences that make up each exon were aligned with the $organism sequence using the tBLASTn program. Finally the putative $organism exons were chained together using an organism- specific maximum gap size (27,000 bp) but no gap penalty. The single best exon chains extending over more than 60% of the query protein were included. All exon chains that matched at least 60% of the protein's amino acids were also included.
tBLASTn is part of the NCBI Blast tool set. For more information on Blast, see Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-410.
Blat was written by Jim Kent. The remaining utilities used to produce this track were written by Jim Kent or Brian Raney.