Hello -
There are many approaches you can use to try and find a promoter with
variable degrees of success. There is extensive literature on this. You
could make profile HMMs and train them with real examples. You could also
use a Gibbs Sampler. There are examples of both in the biojava in anger
pages http://www.biojava.org/docs/bj_in_anger/
Other approaches would be programs like MEME or the technique called
nested MICA developed by Thomas Down of biojava fame which seems to be
very good.
- Mark
Ilueny Santos <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
12/16/2005 04:35 PM
To: biojava-l@biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] Locating promoter regions in sequence of
DNA with Biojava
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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