Genome Res. 2003 Jan;13(1):103-7.

Human-mouse alignments with BLASTZ.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W.

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Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

Erratum in

Genome Res. 2004 Apr;14(4):786.

Abstract

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.

PMID:: 12529312; [PubMed - indexed for MEDLINE]
PMCID: PMC430961

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