Table 1.

Performance of Aligners on the ROSETTA Dataset of 1160 Total Exons in Human and Mouse

Aligner	100% exons	90% exons	70% exons	Time (sec)
DIALIGN	89	96	98	388
MUMmer	0	1	3	17
GLASS	91	97	98	154
AVID	90	95	97	19
BlastZ	94	97	98	17
LAGAN	94	97	98	48

Columns show the percentage of exons annotated in human that are aligned to the orthologous mouse exon over at least 70%, 90%, and 100% of their length, and the time required to align the 129 sequences.