Z-Hunt - Revision history

Christoph: /* External links */

2015-01-23T01:03:33Z

‎External links

Christoph: /* External links */

2014-02-18T18:51:09Z

‎External links

Christoph: /* External links */

2012-02-18T18:33:46Z

‎External links

Christoph: /* Terms */

2008-12-25T07:46:41Z

‎Terms

Christoph at 07:19, 25 December 2008

2008-12-25T07:19:57Z

Christoph at 06:18, 25 December 2008

2008-12-25T06:18:58Z

Christoph at 10:09, 15 February 2008

2008-02-15T10:09:19Z

Christoph: /* External links */

2007-09-30T03:46:52Z

‎External links

Christoph: /* Z-score */

2007-09-17T07:05:24Z

‎Z-score

Christoph: /* Z-score */

2006-08-09T00:00:59Z

‎Z-score

@@ Line 92: / Line 92: @@
 ==External links==
 *[http://gac-web.cgrb.oregonstate.edu/zDNA/ ZHunt Online Server] (''website currently offline'') &mdash; front end by Sandor Maurice; back end by Sandor Maurice and P. Christoph Champ.
 *[http://structure.usc.edu/make-na/ make-na server] &mdash; create custom DNA structures (in PDB format)
 [[Category:Academic Research]]
 [[Category:Portfolio]]

@@ Line 91: / Line 91: @@
 ==External links==
-*[http://gac-web.cgrb.oregonstate.edu/zDNA/ ZHunt Online Server] &mdash; front end by Sandor Maurice; back end by Sandor Maurice and P. Christoph Champ.
+*[http://gac-web.cgrb.oregonstate.edu/zDNA/ ZHunt Online Server] (''website currently offline'') &mdash; front end by Sandor Maurice; back end by Sandor Maurice and P. Christoph Champ.
 *[http://structure.usc.edu/make-na/ make-na server] &mdash; create custom DNA structures (in PDB format)
 [[Category:Academic Research]]
 [[Category:Portfolio]]

← Older revision		Revision as of 18:33, 18 February 2012
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	[[Category:Academic Research]]		[[Category:Academic Research]]
		+	[[Category:Portfolio]]

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 ::[[Image:Partition function.png]]
 ::for propagation of Z-DNA through ''n'' number of dinucleotides, and 0.179 is the &Delta;''Tw'' for each dinucleotide and 0.4 is the &Delta;''Tw'' of the two B&ndash;Z junctions.
 ==Z-score==

@@ Line 1: / Line 1: @@
-'''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].
+'''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="Ho1986">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 name="Champ2004">[[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>. ZHUNT is available for use Online at [http://gac-web.cgrb.oregonstate.edu/zDNA/ 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 "[[wikipedia:Standard score|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.
+Note: The following table is a list of test sequences with their corresponding conformational assignments and Z-scores (now called "''P<sub>Z</sub>''" scores). This "Z-score" should not be confused with the statistical "[[wikipedia:Standard score|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.
 <div style="float:left; margin:0px 20px 20px 0px;">
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@@ Line 50: / Line 68: @@
 |}
 </div>
 ==See also==

@@ Line 1: / Line 1: @@
-'''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].
+'''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==
@@ Line 62: / Line 62: @@
 <small><references/></small>
 ===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''.

@@ Line 1: / Line 1: @@
 '''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].
-== Z-score ==
+==Z-score==
-Note: The following table is a list of test sequences with their corresponding conformational assignments and Z-scores.
+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 "[[wikipedia:Standard score|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.
 <div style="float:left; margin:0px 20px 20px 0px;">
 {| align="center" style="border: 1px solid #999; background-color:#FFFFFF"
@@ Line 51: / Line 51: @@
 </div>
-== See also ==
+==See also==
-* [[Z-DNA]]
+*[[Z-DNA]]
-* [http://en.wikipedia.org/wiki/DNA_supercoil DNA supercoil]
+*[[wikipedia:DNA supercoil]]
-* [http://en.wikipedia.org/wiki/Gibbs_free_energy Gibbs free energy]
+*[[wikipedia:Gibbs free energy]]
-* [http://en.wikipedia.org/wiki/Topoisomerase Topoisomerase]
+*[[wikipedia:Topoisomerase]]
-* [http://en.wikipedia.org/wiki/Linking_number Linking number]
+*[[wikipedia:Linking number]]
-* [http://en.wikipedia.org/wiki/M%C3%B6bius_strip Möbius strip]
+*[[wikipedia:Möbius strip]]
-== References ==
+==References==
 <small><references/></small>
-=== Further reading ===
+===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''.
+*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''.
 ==External links==

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 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>