title: Human-mouse alignments with BLASTZ.
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.
authors.affiliation: Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Schwartz
authors.forename: W James
authors.initials: WJ
authors.lastname: Kent
authors.forename: Arian
authors.initials: A
authors.lastname: Smit
authors.forename: Zheng
authors.initials: Z
authors.lastname: Zhang
authors.forename: Robert
authors.initials: R
authors.lastname: Baertsch
authors.forename: Ross C
authors.initials: RC
authors.lastname: Hardison
authors.forename: David
authors.initials: D
authors.lastname: Haussler
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
mesh_terms: D000818:Animals; D003628:Database Management Systems / Q000295:instrumentation; D016678:Genome; D015894:Genome, Human; D006801:Humans; D051379:Mice; D016415:Sequence Alignment / Q000295:instrumentation* / Q000379:methods*; D012985:Software Design; D012986:Software Validation