Introduction

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.

Publications

  1. Human-mouse alignments with BLASTZ.
    Cite this
    Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W, 2003-01-01 - Genome research

Credits

  1. Scott Schwartz
    Developer

    Department of Computer Science and Engineering, The Pennsylvania State University, United States of America

  2. W James Kent
    Developer

  3. Arian Smit
    Developer

  4. Zheng Zhang
    Developer

  5. Robert Baertsch
    Developer

  6. Ross C Hardison
    Developer

  7. David Haussler
    Developer

  8. Webb Miller
    Investigator

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Summary
AccessionBT002534
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Submitted ByWebb Miller