This track contains tBLASTn alignments of the peptides from the predicted and
known genes identified in the hg18 UCSC Genes track.
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
cow sequence using the tBLASTn program.
Finally, the putative cow exons were chained together using an
organism-specific maximum gap size but no gap penalty. The single best exon
chains extending over more than 60% of the query protein were included. Exon
chains that extended over 60% of the query and 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.