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> | + | <div style="float:left; margin:0px 20px 20px 0px;"> |
| + | {| align="center" style="border: 1px solid #999; background-color:#FFFFFF" | ||
| + | |-align="center" bgcolor="#1188ee" | ||
| + | |- | ||
| + | |<pre> | ||
| + | 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 | | ||
| + | </pre> | ||
| + | || 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> | ||
| + | |} | ||
| + | </div> | ||
== 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
- ↑ 1.0 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.
