Table 2.

Comparison of Genome Coverage

	chr20	CDS	3′UTR	5′UTR	upstream
Blastz all	40.5%	98.5%	87.1%	89.0%	87.2%
Blastz tight	5.6%	92.5%	26.0%	39.6%	28.3%
PH all	29.7%	95.5%	55.0%	59.3%	52.5%
PH tight	5.0%	91.2%	25.1%	36.3%	25.2%
transl. BLAT	5.8%	90.3%	29.2%	38.4%	27.2%

Percentage of human chromosome 20, and various gene features on this chromosome covered by BLASTZ, PatternHunter, and translated BLAT in alignments between this chromosome and the mouse genome. The CDS, 3′ UTR, 5′ UTR, and upstream columns are based on RefSeq () mRNA defined genes available at the Human Genome Browswer (http://genome.ucsc.edu; ). The upstream column is 200 bases upstream of transcription start for genes in which there is an annotated 5′ UTR. For the BLASTZ and PatternHunter alignments, subsets relatively specific to coding regions were constructed by rescoring the alignments using the substitution scores

a gap open score of −2000, a gap extension score of −50, and a threshold of 3400.