Difference between revisions of "Z-Hunt"

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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>
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Sequence/conf. assignments  | Z-score
 +
----------------------------|------------
 +
CGCGCGCGCGCGCGCGCGCGCGCG    | 2 x 10e+11
 +
ASASASASASASASASASASASAS    |
 +
                            |
 +
CGCGCGCGCGCG                | 4 x 10e+07
 +
ASASASASASAS                |
 +
                            |
 +
CACACACACACACACACACACACA    | 2 x 10e+05
 +
ASASASASASASASASASASASAS    |
 +
                            |
 +
CACACACACACA                | 2 x 10e+04
 +
ASASASASASAS                |
 +
                            |
 +
CGCGCGCGCGCG GCGCGCGCGCGC  | 2 x 10e+08
 +
ASASASASASAS SASASASASASA  |
 +
                            |
 +
CGCGCG GCGCGC CGCGCG GCGCGC | 7 x 10e+04
 +
ASASAS SASASA ASASAS SASASA |
 +
                            |
 +
*  *  *  *  *  *      |
 +
CCCGCCCGCCCGCCCGCCCGCCCG    | 8 x 10e+04
 +
ASASASASASASASASASASASAS    |
 +
                            |
 +
  *  *  *  *  *  *    |
 +
CAGGCAGGCAGGCAGGCAGGCAGG    | 1 x 10e+03
 +
ASASASASASASASASASASASAS    |
 +
                            |
 +
* * * * * * * * * * * *    |
 +
CCCCCCCCCCCCCCCCCCCCCCCC    | 52
 +
ASASASASASASASASASASASAS    |
 +
                            |
 +
ATATATATATATATATATATATAT    | 38
 +
SASASASASASASASASASASASA    |
 +
                            |
 +
AAAAAAAAAAAAAAAAAAAAAAAA    | 3 x 10e-07
 +
ASASASASASASASASASASASAS    |
 +
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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>
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== See also ==
 
== See also ==

Revision as of 23:59, 8 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]
Sequence/conf. assignments  | Z-score
----------------------------|------------
CGCGCGCGCGCGCGCGCGCGCGCG    | 2 x 10e+11
ASASASASASASASASASASASAS    |
                            |
CGCGCGCGCGCG                | 4 x 10e+07
ASASASASASAS                |
                            |
CACACACACACACACACACACACA    | 2 x 10e+05
ASASASASASASASASASASASAS    |
                            |
CACACACACACA                | 2 x 10e+04
ASASASASASAS                |
                            |
CGCGCGCGCGCG GCGCGCGCGCGC   | 2 x 10e+08
ASASASASASAS SASASASASASA   |
                            |
CGCGCG GCGCGC CGCGCG GCGCGC | 7 x 10e+04
ASASAS SASASA ASASAS SASASA |
                            |
 *   *   *   *   *   *      |
CCCGCCCGCCCGCCCGCCCGCCCG    | 8 x 10e+04
ASASASASASASASASASASASAS    |
                            |
  *   *   *   *   *   *     |
CAGGCAGGCAGGCAGGCAGGCAGG    | 1 x 10e+03
ASASASASASASASASASASASAS    |
                            |
 * * * * * * * * * * * *    |
CCCCCCCCCCCCCCCCCCCCCCCC    | 52
ASASASASASASASASASASASAS    |
                            |
ATATATATATATATATATATATAT    | 38
SASASASASASASASASASASASA    |
                            |
AAAAAAAAAAAAAAAAAAAAAAAA    | 3 x 10e-07
ASASASASASASASASASASASAS    |
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.