Human-mouse alignments with BLASTZ.

Scott Schwartz, W. James Kent, Arian Smit, Zheng Zhang, Robert Baertsch, Ross C. Hardison, David Haussler, Webb Miller

Research output: Contribution to journalArticlepeer-review

977 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)103-107
Number of pages5
JournalGenome research
Issue number1
StatePublished - Jan 2003

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)


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