## Description

This track contains tBLASTn alignments of the peptides from the predicted and known genes identified in the hg18 UCSC Genes track.

## Methods

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 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.

## Credits

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.