Difference between revisions of "Z-Hunt"

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'''Z-Hunt''' (aka '''ZHunt''') is an algorithm for predicting the propensity of DNA to flip from the B-form to the [[Z-DNA|Z-form]]. The original algorithm was written by [[Dr. P. Shing Ho Laboratory|Dr. P. Shing Ho]] in 1986<ref>Ho PS, Ellison MJ, Quigley GJ, Rich A (1986). A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. ''EMBO J, 5(10):2737-2744''.</ref> and was later developed by Tracy Camp, [[Christoph Champ|P. Christoph Champ]], Sandor Maurice, and Jeffrey M. Vargason for genome-wide mapping of [[Z-DNA]] (with P. Shing Ho as the principal investigator)<ref>[[Christoph Champ|Champ PC]], Maurice S, Vargason JM, Camp T, Ho PS (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. ''Nucleic Acids Research, 32(22):6501-6510''.</ref>. Z-Hunt is available for use Online at [http://gac-web.cgrb.oregonstate.edu/zDNA/ ZHunt Online].
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'''Z-Hunt''' (aka '''ZHunt''') is an algorithm for predicting the propensity of DNA to flip from the B-form to the [[Z-DNA|Z-form]]. The original algorithm was written by [[Dr. P. Shing Ho Laboratory|Dr. P. Shing Ho]] in 1986<ref name=Ho86>Ho PS, Ellison MJ, Quigley GJ, Rich A (1986). A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. ''EMBO J, 5(10):2737-2744''.</ref> and was later developed by Tracy Camp, [[Christoph Champ|P. Christoph Champ]], Sandor Maurice, and Jeffrey M. Vargason for genome-wide mapping of [[Z-DNA]] (with P. Shing Ho as the principal investigator)<ref>[[Christoph Champ|Champ PC]], Maurice S, Vargason JM, Camp T, Ho PS (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. ''Nucleic Acids Research, 32(22):6501-6510''.</ref>. Z-Hunt is available for use Online at [http://gac-web.cgrb.oregonstate.edu/zDNA/ ZHunt Online].
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== Z-score ==
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Note: The following table is a list of test sequences with their corresponding conformational assignments and Z-scores.
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<div style="float:left; margin:0px 20px 20px 0px;">
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{| align="center" style="border: 1px solid #999; background-color:#FFFFFF"
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|-align="center" bgcolor="#1188ee"
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!Sequence/conformation assignments
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!Z-score
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|-
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|<pre>CGCGCGCGCGCGCGCGCGCGCGCG
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ASASASASASASASASASASASAS</pre>
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|| 2 x 10<sup>11</sup>
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|- bgcolor="#eee"
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|<pre>
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CGCGCGCGCGCG
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ASASASASASAS</pre>
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|| 4 x 10<sup>7</sup>
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|-
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|<pre>
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CACACACACACACACACACACACA
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ASASASASASASASASASASASAS</pre>
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|| 2 x 10<sup>5</sup>
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|- bgcolor="#eee"
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|<pre>
 +
CACACACACACA
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ASASASASASAS</pre>
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|| 2 x 10<sup>4</sup>
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|-
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|<pre>
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CGCGCGCGCGCG GCGCGCGCGCGC
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ASASASASASAS SASASASASASA</pre>
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|| 2 x 10<sup>8</sup>
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|- bgcolor="#eee"
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|<pre>
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CGCGCG GCGCGC CGCGCG GCGCGC
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ASASAS SASASA ASASAS SASASA</pre>
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|| 7 x 10<sup>4</sup>
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|-
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|<pre>
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*  *  *  *  *  *
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CCCGCCCGCCCGCCCGCCCGCCCG
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ASASASASASASASASASASASAS</pre>
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|| 8 x 10<sup>4</sup>
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|- bgcolor="#eee"
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|<pre>
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  *  *  *  *  *  *
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CAGGCAGGCAGGCAGGCAGGCAGG
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ASASASASASASASASASASASAS</pre>
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|| 1 x 10<sup>3</sup>
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|-
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|<pre>
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* * * * * * * * * * * *
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CCCCCCCCCCCCCCCCCCCCCCCC
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ASASASASASASASASASASASAS</pre>
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|| 52
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|- bgcolor="#eee"
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|<pre>
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ATATATATATATATATATATATAT
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SASASASASASASASASASASASA</pre>
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|| 38
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|-
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|<pre>
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AAAAAAAAAAAAAAAAAAAAAAAA
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ASASASASASASASASASASASAS</pre>
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|| 3 x 10<sup>-7</sup>
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|}
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<div align="center">''Source: Ho, et al.<ref name=Ho86>Ho PS, Ellison MJ, Quigley GJ, Rich A (1986). A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. ''EMBO J, 5(10):2737-2744''.</ref>''</div>
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</div>
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Various test sequences are shown with their corresponding Z-score as assigned by Z-hunt [version 1]. Z-scores are defined as the number of random base pairs that must be scanned, on average, to find a sequence with equal or better Z-forming capacity relative to the sequence in question. The conformation selected by Z-hunt for each nucleotide (A for ''anti'' and S for ''syn'') are indicated below each sequence. Bases which deviate from perfect purine-pyrimidine alternation are designated by dots above that nucleotide. Discontinuities in the conformational phases produced by Z-Z junctions are represented by gaps separating the sequence.<ref name=Ho86>Ho PS, Ellison MJ, Quigley GJ, Rich A (1986). A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. ''EMBO J, 5(10):2737-2744''.</ref>
  
 
== See also ==
 
== See also ==

Revision as of 23:36, 1 August 2006

Z-Hunt (aka ZHunt) is an algorithm for predicting the propensity of DNA to flip from the B-form to the Z-form. The original algorithm was written by Dr. P. Shing Ho in 1986[1] and was later developed by Tracy Camp, P. Christoph Champ, Sandor Maurice, and Jeffrey M. Vargason for genome-wide mapping of Z-DNA (with P. Shing Ho as the principal investigator)[2]. Z-Hunt is available for use Online at ZHunt Online.

Z-score

Note: The following table is a list of test sequences with their corresponding conformational assignments and Z-scores.

Sequence/conformation assignments Z-score 
CGCGCGCGCGCGCGCGCGCGCGCG
ASASASASASASASASASASASAS
 2 x 1011 
CGCGCGCGCGCG
ASASASASASAS
 4 x 107 
CACACACACACACACACACACACA
ASASASASASASASASASASASAS
 2 x 105 
CACACACACACA
ASASASASASAS
 2 x 104 
CGCGCGCGCGCG GCGCGCGCGCGC
ASASASASASAS SASASASASASA
 2 x 108 
CGCGCG GCGCGC CGCGCG GCGCGC
ASASAS SASASA ASASAS SASASA
 7 x 104 
 *   *   *   *   *   *
CCCGCCCGCCCGCCCGCCCGCCCG
ASASASASASASASASASASASAS
 8 x 104 
  *   *   *   *   *   *
CAGGCAGGCAGGCAGGCAGGCAGG
ASASASASASASASASASASASAS
 1 x 103 
 * * * * * * * * * * * *
CCCCCCCCCCCCCCCCCCCCCCCC
ASASASASASASASASASASASAS
 52 
ATATATATATATATATATATATAT
SASASASASASASASASASASASA
 38 
AAAAAAAAAAAAAAAAAAAAAAAA
ASASASASASASASASASASASAS
 3 x 10-7
Source: Ho, et al.[1]

Various test sequences are shown with their corresponding Z-score as assigned by Z-hunt [version 1]. Z-scores are defined as the number of random base pairs that must be scanned, on average, to find a sequence with equal or better Z-forming capacity relative to the sequence in question. The conformation selected by Z-hunt for each nucleotide (A for anti and S for syn) are indicated below each sequence. Bases which deviate from perfect purine-pyrimidine alternation are designated by dots above that nucleotide. Discontinuities in the conformational phases produced by Z-Z junctions are represented by gaps separating the sequence.[1]

See also

References

  1. ↑ 1.0 1.1 1.2 Ho PS, Ellison MJ, Quigley GJ, Rich A (1986). A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. EMBO J, 5(10):2737-2744.
  2. ↑ Champ PC, Maurice S, Vargason JM, Camp T, Ho PS (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Research, 32(22):6501-6510.

Further reading

  • Ho PS (1994). The non-B-DNA structure of d(CA/TG)n does not differ from that of Z-DNA. Proc Natl Acad Sci USA, 91(20):9549-9553.
  • Schroth GP, Chou PJ, Ho PS (1992). Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes. J Biol Chem, 267(17):11846-55.

External links

  • ZHunt Online Server — front end by Sandor Maurice; back end by Sandor Maurice and P. Christoph Champ.
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