TY  - JOUR
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
Y1  - 2003/01/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 103 
EP  - 107 
DO  - 10.1101/gr.809403 
VL  - 13 
IS  - 1 
UR  - http://genome.cshlp.org/content/13/1/103.abstract 
N2  - 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. 
ER  -