How to set window size of DNA

[Yoonsoo Hahn]

hum..I wonder whether i can understand myself in English.

I'm trying to find any correlations between DNA sequence properties.
But, It's window-size sensitive, that is, if the window size is big
the property becomes to the average value of whole sequence.
If the window size is small the variance of the property is too big.

for eg. I tried to find the relationship between A and B.

(1) when the window size is small
B |
  |    *       *
  | *   *
  |  *     *  *
  |       * *    *
  |      *   *
  |
  +--------------------
                     A
(2) when the window size is big
B |
  |            
  |       *
  |      **** 
  |       **
  |           
  |
  +--------------------
                     A
(3) when the window size is appropriate
    (this is what i want to find)
B |
  |            
  |           ****
  |       ****
  |    ***  
  |  **       
  |
  +--------------------
                     A

I typically choose 100 bp or 500 bp or 1 kb for the window size.
And now I want to know IF THERE IS ANY GENERAL SIZE OF THE WINDOW for
this kind of analysis.

Thanks in advance.

--
    ____________________________
___/ LIFE IS SHORT, DNA IS LONG \_____________________________________________
-. .-.   .-. .-.   .-. .-.   .  |  Yoonsoo Hahn                              |
||X|||\ /|||X|||\ /|||X|||\ /|  |  Laboratory of Molecular Genetics          |
|/ \|||X|||/ \|||X|||/ \|||X||  |  Department of Biological Sciences, KAIST  |
'   `-' `-'   `-' `-'   `-' `-  |  yshan at sorak.kaist.ac.kr, +82-42-869-5261  |