Difference between revisions of "Z-Hunt"
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| − | '''Z-Hunt''' | + | '''ZHUNT''' (aka '''Z-Hunt''' or '''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]. |
==Z-score== | ==Z-score== | ||
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<small><references/></small> | <small><references/></small> | ||
===Further reading=== | ===Further reading=== | ||
| + | *Ho PS (2008). "Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure". ''Methods, [Epub ahead of print]''. PMID: 18848994. {{doi|10.1016/j.ymeth.2008.09.007}} | ||
*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''. | *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''. | *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''. | ||
Revision as of 06:18, 25 December 2008
ZHUNT (aka Z-Hunt or 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. This "Z-score" should not be confused with the statistical "Standard score". Here, it describes the propensity of a given sequence to adopt the left-handed form of DNA; it is simply a probability score.
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
- Z-DNA
- wikipedia:DNA supercoil
- wikipedia:Gibbs free energy
- wikipedia:Topoisomerase
- wikipedia:Linking number
- wikipedia:Möbius strip
References
- ↑ 1.0 1.1 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 (2008). "Thermogenomics: Thermodynamic-based approaches to genomic analyses of DNA structure". Methods, [Epub ahead of print]. PMID: 18848994. DOI:10.1016/j.ymeth.2008.09.007
- 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.
- make-na server — create custom DNA structures (in PDB format)
