Z-Hunt
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 |
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
- ↑ 1.0 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.
- ↑ 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.
