RT Journal
A1 Schwartz, Scott
A1 Kent, W. James
A1 Smit, Arian
A1 Zhang, Zheng
A1 Baertsch, Robert
A1 Hardison, Ross C.
A1 Haussler, David
A1 Miller, Webb
T1 Human–Mouse Alignments with BLASTZ
JF Genome Research 
JO Genome Research 
YR 2003 
FD January 01 
VO 13 
IS 1 
SP 103 
OP 107 
DO 10.1101/gr.809403 
UL http://genome.cshlp.org/content/13/1/103.abstract 
AB The Mouse Genome Analysis Consortium aligned the human and mouse genome sequences for a variety of purposes, using alignment programs that suited the various needs. For investigating issues regarding genome evolution, a particularly sensitive method was needed to permit alignment of a large proportion of the neutrally evolving regions. We selected a program called BLASTZ, an independent implementation of the Gapped BLAST algorithm specifically designed for aligning two long genomic sequences. BLASTZ was subsequently modified, both to attain efficiency adequate for aligning entire mammalian genomes and to increase its sensitivity. This work describes BLASTZ, its modifications, the hardware environment on which we run it, and several empirical studies to validate its results.