[Biojava-l] Locating promoter regions in sequence of DNA with Biojava

[Ilueny Santos]

Hello to all, 
 
 First would like to be thankful all, in special to the Mark and Gregory, for having answered.  
 
 Explaining of form more detailed my doubt: 
      I was trying to locate definitive regions in a DNA sequence (-10 box and -35 box).  These regions are small stretches of 6 pairs of bases (pb) and are thus called by being generally the 10 pb and 35 pb, respectively, upstream of +1 (ATG) and the presence of them in the sequence strong characterizes the existence of a promoter.  
 
     The problem is that they are not steady, for example:
 region -10 box normally is presented as TATAAT but it can have variations in form TATAAG in such a way or TATTAT how much in its positioning in relation to start codon (+1 ATG) 
 
 
 Leaving of Displayed I ask:  
 it will be that I obtain, using biojava it, to make one algorítmo capable to locate unstable regions (in such a way in the form how much in its positioning) in DNA sequences? 
 
 
 I am thankful all one more time that will be able to help. 
 
 PS.:  Gregory favours, already I am studying Regular Expressions and...,  Mark, the bayesiano classifier already is fact, but, followed its tip, 
 I go to also study the package org.biojava.dist because it can be useful of some form, thanks.
 

		
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