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Published online before print December 30, 2002, 10.1101/gr.809403
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Vol 13, Issue 1, 103-107, January 2003

METHODS

Human–Mouse Alignments with BLASTZ

Scott Schwartz1, W. James Kent2, Arian Smit3, Zheng Zhang4, Robert Baertsch2, Ross C. Hardison5, David Haussler6 and Webb Miller1,7

1Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; 2Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA;3 Institute for Systems Biology, Seattle, Washington 98103, USA; 4Paracel Inc., Pasadena, California 91106, USA;5 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; 6Howard Hughes Medical Institute, 321 Applied Sciences, University of California, Santa Cruz, California 95064, USA

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.

7 Corresponding author.

E-MAIL webb{at}bio.cse.psu.edu; FAX (814) 865-3176.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.809403. Article published online before print in December 2002.


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