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cgr [2009/07/16 09:18]
admin
cgr [2014/01/18 07:44] (current)
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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 ====
  
 This program creates an image showing the abundance of all k-mers (oligonucleotides of length k) in a given sequence. For example, for tetramers (k=4), resulting image is composed of 4^4 = 256 boxes, each representing an oligomer. Oligomer name and abundance is written within these boxes, and abundance is also visualized with the box color, from white (none) to black (highly frequent). This program creates an image showing the abundance of all k-mers (oligonucleotides of length k) in a given sequence. For example, for tetramers (k=4), resulting image is composed of 4^4 = 256 boxes, each representing an oligomer. Oligomer name and abundance is written within these boxes, and abundance is also visualized with the box color, from white (none) to black (highly frequent).
 +
 +{{:​kmer_table.png|}}
  
 This k-mer table is alternatively known as the FCGR (frequency matrices extracted from Chaos Game Representation). This k-mer table is alternatively known as the FCGR (frequency matrices extracted from Chaos Game Representation).
  
 Position of the oligomers can be recursively located as follows: Position of the oligomers can be recursively located as follows:
-  * For each letter in an oligomer, a box is subdivided into four quadrants, where A is upper left, T is lower right, G is upper right, and C is lower left. Therefore, oligomer ​ATGC is in the+  * For each letter in an oligomer, a box is subdivided into four quadrants, where A is upper left, T is lower right, G is upper right, and C is lower left. Therefore, oligomer ​ACGT is in the
  
       A = upper left quadrant       A = upper left quadrant
-      T = lower right within the above quadrant 
-      G = upper right within the above quadrant 
       C = lower left within the above quadrant       C = lower left within the above quadrant
 +      G = upper right within the above quadrant
 +      T = lower right within the above quadrant
 +
 +{{:​kmer-ex.png?​400|}}
 +
 +==== Zoomable Google Maps ====
 +
 +For CGR and k-mer tables to be useful as generalized scale-independent Markov probability table, it is critical for a user to be able to locate the oligonucleotides of interest quickly within the complex image. For this purpose, we have implemented CGR as zoomable Google Maps. 
 +
 +{{:​googlemapcgr.png|}}
 +
 +Here you can easily pan and zoom the large image with the same user interface as the familiar Google Maps; therefore, you can use the controller located in the top left corner for panning and zooming, or double clicking or use mouse scroll wheel for zooming, and so on.
 +
 +As an addition, we have implemented a search capability. The search box is located at the top center of the map, where you can type in oligonucleotide sequences to perform incremental search/​highlight over the map. For example, typing "​CG"​ in the search box immediately highlights the position of oligomers starting with letters "​CG"​.
 +
 +{{:​snapz_pro_xscreensnapz001.png|}}
 +
 +You can use "​N"​ to represent wild card nucleotide. Therefore, searching for "​NCG"​ highlights four regions corresponding to "​ACG",​ "​TCG",​ "​GCG",​ and "​CCG"​. With this feature, users can quickly locate the oligonucleotide of interest, and observe the Markov chain probabilities following the specified nucleotides.
  
 +{{:​snapz_pro_xscreensnapz002.png|}}
  
 ==== Chaos Game Representation for five prokaryotes ==== ==== Chaos Game Representation for five prokaryotes ====
cgr.1247735912.txt.gz · Last modified: 2014/01/18 07:44 (external edit)