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cgr [2009/07/16 11:45]
admin
cgr [2009/12/05 15:31]
admin
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 ====== A Web Server for Zoomable Chaos Game Represenations ====== ====== A Web Server for Zoomable Chaos Game Represenations ======
-===== Overview ​=====+===== Publication ​===== 
 +This software is described in the following manuscript:  
 +[[http://​www.scfbm.org/​content/​4/​1/​6|Arakawa K, Oshita K, Tomita M, "A web server for interactive and zoomable Chaos Game Representation images",​ Source Code for Biology and Medicine, 2009, 4:6.]]
  
 +===== Browser Compatibility =====
 +__**Internet Explorer is NOT supported for Google Map view. Please use Safari or Firefox. **__
 +===== Quick Demo =====
 +  * [[http://​ws.g-language.org/​db/​cgr/​NC_000913/​|Escherichia coli K12 genome]]
 +  * [[http://​ws.g-language.org/​db/​cgr/​NC_000964/​|Bacillus subtillis genome]]
 +  * [[http://​ws.g-language.org/​db/​cgr/​NC_005070/​|Synechococcus sp. genome]]
 +  * [[http://​ws.g-language.org/​db/​cgr/​NC_003413/​|Pyrococcus furiosus genome]]
 +  * [[http://​ws.g-language.org/​db/​cgr/​NC_000908/​|Mycoplasma genitalium genome]]
 +  * [[http://​ws.g-language.org/​db/​cgr/​NC_001133/​|Saccharomyces cerevisiae chromosome I]]
 +  * [[http://​ws.g-language.org/​db/​cgr/​NT_033778/​|Drosophila melanogaster chromosome 2R]]
 +  * [[http://​ws.g-language.org/​db/​cgr/​NT_011512/​|Homo sapiens chromosome 21]]
 +
 +
 +===== Overview =====
 ==== Chaos Game Representation ==== ==== Chaos Game Representation ====
  
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            C: (-1, -1) lower left            C: (-1, -1) lower left
  
-  * For each nucleotide, move and mark the new location which is halfway between the current location and the nucleotide. For example, if the first letter is A, position is moved from (0,0) to midpoint between (-1, 1) and (0,0), which is (-0.5, 0.5).+  * For each nucleotide ​(in reverse order to match k-mer table; i.e., match forward Markov chain), move and mark the new location which is halfway between the current location and the nucleotide. For example, if the last letter is T, position is moved from (0,0) to midpoint between (1, -1) and (0,0), which is (0.5, -0.5).
   * Repeat this procedure for all nucleotides.   * Repeat this procedure for all nucleotides.
 +
 +{{:​figure1.001.png?​400}}
 +
 ==== k-mer table ==== ==== k-mer table ====
  
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       G = upper right within the above quadrant       G = upper right within the above quadrant
       T = lower right within the above quadrant       T = lower right within the above quadrant
 +
 +{{:​kmer-ex.png?​400|}}
  
 ==== Zoomable Google Maps ==== ==== Zoomable Google Maps ====
cgr.txt · Last modified: 2014/01/18 07:44 (external edit)