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From: "Vivek " <vivek_mutalik@yahoo.com>
Newsgroups: comp.soft-sys.matlab
Subject: Re: Is this kind of regression possible?
Date: Sat, 1 Dec 2007 00:51:50 +0000 (UTC)
Organization: University of California, San Francisco
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"Vivek " <vivek_mutalik@yahoo.com> wrote in message
<fio8nm$6k4$1@fred.mathworks.com>...
> Hi,
> 
> I m having difficulty in formulating following problem. If
> you have any suggestions that'll be great.
> 
> Ive set of "aligned DNA sequences" with their activities. I
> want to do regression so that i can get weights for each
> base (A,C,G,T). This may help me in understanding which
> bases are 'important and contribute' towards measured
activity. 
> Example: My activity VS sequence table looks like
> (1) 08 ACAG
> (2) 10 ATTC
> (3) 05 GGTA
> (4) 04 CCGT
> (5) ... ....
>    ....etc
> 
> My solution would be: to minimize the residual sum of square:
> (here W is weight of that particular base, which is what im
> trying to estimate)
> 
> = [8 - (W1A + W2C + W3A + W4G)]^2 + [10 - (W1A + W2T + W3T
> +W4C)]^2 + and so on.
> 
> to reduce the parameters to be determined, I can substract
> weight of 'T' from each of weights and finally add sum of
> all 'T' (as if 'T' is in all positions).
> 
> That is:
> 
> = [8 - (W1A-W1T + W2C-W2T + W3A-W3T + W4G-W4T) +
> (W1T+W2T+W3T+W4T)]^2
>  +
> [10 - (W1A-W1T + W4C -W1T) + (W1T+W2T+W3T+W4T) ]^2
> 
> + so on;
> 
> Is it making any sense? So by this way, i was thinking of
> getting weights for all bases by using some kind of residual
> minimizing function. Is it possible ?

...............................................

Can it be solved by optimization toolbox ?