Z curve

The Z curve (or Z-curve) method is a bioinformatics algorithm for genome analysis. The Z-curve is a three-dimensional curve that constitutes a unique representation of a DNA sequence, i.e., for the Z-curve and the given DNA sequence each can be uniquely reconstructed from the other.[1] The resulting curve has a zigzag shape, hence the name Z-curve. The Z-curve method has been used in many different areas of genome research, such as replication origin identification,[2][3][4][5] ab initio gene prediction,[6] isochore identification,[7] genomic island identification[8] and comparative genomics.[9]

References

  1. ↑ Zhang CT, Zhang R, Ou HY (2003). "The Z curve database: a graphic representation of genome sequences". Bioinformatics 19 (5): 593–99. doi:10.1093/bioinformatics/btg041. PMID 12651717.
  2. ↑ Zhang R, Zhang CT (2005). "Identification of replication origins in archaeal genomes based on the Z-curve method". Archaea 1 (5): 335–46. doi:10.1155/2005/509646. PMC 2685548. PMID 15876567.
  3. ↑ Zhang R, Zhang CT (September 2002). "Single replication origin of the archaeon Methanosarcina mazei revealed by the Z curve method". Biochem. Biophys. Res. Commun. 297 (2): 396–400. doi:10.1016/S0006-291X(02)02214-3. PMID 12237132.
  4. ↑ Zhang R, Zhang CT (March 2003). "Multiple replication origins of the archaeon Halobacterium species NRC-1". Biochem. Biophys. Res. Commun. 302 (4): 728–34. doi:10.1016/S0006-291X(03)00252-3. PMID 12646230.
  5. ↑ Worning P, Jensen LJ, Hallin PF, Staerfeldt HH, Ussery DW (February 2006). "Origin of replication in circular prokaryotic chromosomes". Environ. Microbiol. 8 (2): 353–61. doi:10.1111/j.1462-2920.2005.00917.x. PMID 16423021.
  6. ↑ Guo FB, Ou HY, Zhang CT (2003). "ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes". Nucleic Acids Research 31 (6): 1780–89. doi:10.1093/nar/gkg254. PMC 152858. PMID 12626720.
  7. ↑ Zhang CT, Zhang R (2004). "Isochore structures in the mouse genome". Genomics 83 (3): 384–94. doi:10.1016/j.ygeno.2003.09.011. PMID 14962664.
  8. ↑ Zhang R, Zhang CT (2004). "A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I". Bioinformatics 20 (5): 612–22. doi:10.1093/bioinformatics/btg453. PMID 15033867.
  9. ↑ Zhang R, Zhang CT (2003). "Identification of genomic islands in the genome of Bacillus cereus by comparative analysis with Bacillus anthracis". Physiological Genomics 16 (1): 19–23. doi:10.1152/physiolgenomics.00170.2003. PMID 14600214.

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