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Comparative Study
. 2003 Jan;13(1):103-7.
doi: 10.1101/gr.809403.

Human-mouse alignments with BLASTZ

Scott Schwartz  1 , W James Kent, Arian Smit, Zheng Zhang, Robert Baertsch, Ross C Hardison, David Haussler, Webb Miller
Affiliations
Comparative Study

V体育官网 - Human-mouse alignments with BLASTZ

Scott Schwartz et al. Genome Res. 2003 Jan.

Erratum in (VSports在线直播)

  • Genome Res. 2004 Apr;14(4):786

"V体育官网入口" 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 VSports手机版. 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. .

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Figures

Figure 1.
Figure 1.
BLASTZ in a nutshell.
See this image and copyright information in PMC

"V体育官网" References

    1. Altschul S.F., Madden, T.L., Schaffer, A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST—a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. - PMC - PubMed
    1. Chiaromonte, F., Yap, V.-B., and Miller, W. 2002. Scoring pairwise genomic sequence alignments. Pacific Symp. Biocomput. 115–126. - PubMed
    1. Elnitski, L., Hardison, R.C., Li, J., Yang, S., Kolbe, D., Eswara, P., O'Connor, M.J., Schwartz, S., Miller, W., and Chiaromonte, F. 2003. Distinguishing regulatory DNA from neutral sites. Genome Res. (this issue). - PMC - PubMed
    1. Hardison, R.C., Roskin, K., Yang, S., Diekhans, M., Kent, W.J., Weber, R., Elnitski, L., Li, J., O'Connor, M., Kolbe, D., et al. 2003. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. (this issue). - PMC - PubMed
    1. Huang, X., Pevzner, P., and Miller, W. 1994. Parametric recomputing in alignment graphs. Combinatorial Pattern Matching (Springer Lecture Notes in Computer Science, 807), 87–101.

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