<p>"My question is what is the importance/effect of amino acid A occuring at position I in the sequence with respect to the model?"</p>

<p>I suggest <a href="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.65.4858&amp;rep=rep1&amp;type=pdf" rel="nofollow">Monotony and Surprise</a> by Apostolico for the modeling of importance of words appearing at certain positions, or in certain patterns.  Beyond that, I'm not sure what you're looking for.</p>

CC BY-SA 2.5
2010-10-07T20:18:02.323Z
This link is behind a paywall I think, but is a less technical explanation of the approach.  http://www.springerlink.com/content/nn13140321803528/fulltext.pdf
Aaron Sterling
CC BY-SA 2.5
2010-10-07T20:14:29.827Z
2010-10-07T20:14:29.827Z
Aaron Sterling
<p>I work with amino acid sequences and I want to use a self-made model to tell me something about it, let's call it f(seq). Now I want to know the contribution of every position in the sequence onto the model. E.q. My question is what is the importance/effect of amino acid A occurring at position I in the sequence with respect to the model? </p>

<p>How do I visualize something like that?</p>

<p>I want to use my model also on several sequences of differing lengths. Somehow this throws a monkey wrench into my plans of using a neural net...</p>

<p>My question is simple yet I did not find anything about it. Pointers would be appreciated. Or any comment you might have. This whole idea of mine is pretty unfinished and I don't really know yet what I want. So feel free to criticize, I will update the question accordingly.  </p>

CC BY-SA 2.5
2010-10-07T09:53:23.920Z
What kind of model do you have, in particular deterministic or probabilistic?

How would you like to measure contribution? I can imagine using an independence measure if every position and $f(seq)$ are treated as random variables. If $f(seq)$ is independent of $seq[i]$ the $i$th symbol does not yield a contribution.
Raphael
CC BY-SA 2.5
2010-10-07T10:22:43.590Z
You are more likely to find answers at http://stats.stackexchange.com/ for this kind of question.
András Salamon
CC BY-SA 2.5
2010-10-07T10:36:20.180Z
the best thing would be to keep the model abstract. but it will be a probabilistic one probably. I will look into independence measures (: However i think the sequence positions should not be regarded as independent. I would like to find some pattern or sth that has a bigger contribution than a single amino acid.
tarrasch
CC BY-SA 2.5
2010-10-07T10:36:58.477Z
i will repost the question at stats.stackexchange and pool the answers. thanks
tarrasch
CC BY-SA 2.5
2010-10-07T20:20:03.577Z
Question is too vague to be answerable.
Warren Schudy
<st.statistics><ne.neural-evol>
Analysis of variables of varying numbers
tarrasch
# Analysis of variables of varying numbers

(Asked by: username_0 on 2010-10-07)

I work with amino acid sequences and I want to use a self-made model to tell me something about it, let's call it f(seq). Now I want to know the contribution of every position in the sequence onto the model. E.q. My question is what is the importance/effect of amino acid A occurring at position I in the sequence with respect to the model?

How do I visualize something like that?

I want to use my model also on several sequences of differing lengths. Somehow this throws a monkey wrench into my plans of using a neural net...

My question is simple yet I did not find anything about it. Pointers would be appreciated. Or any comment you might have. This whole idea of mine is pretty unfinished and I don't really know yet what I want. So feel free to criticize, I will update the question accordingly.

**Tags:** st.statistics, ne.neural-evol
> **Comments:**
> **username_1**: What kind of model do you have, in particular deterministic or probabilistic?  How would you like to measure contribution? I can imagine using an independence measure if every position and $f(seq)$ are treated as random variables. If $f(seq)$ is independent of $seq[i]$ the $i$th symbol does not yield a contribution.  
> **username_2**: You are more likely to find answers at http://stats.stackexchange.com/ for this kind of question.  
> **username_0**: the best thing would be to keep the model abstract. but it will be a probabilistic one probably. I will look into independence measures (: However i think the sequence positions should not be regarded as independent. I would like to find some pattern or sth that has a bigger contribution than a single amino acid.  
> **username_0**: i will repost the question at stats.stackexchange and pool the answers. thanks  
> **username_3**: Question is too vague to be answerable.  

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## 1 answers

### Answer by username_4 on 2010-10-07. Score: 4 | Accepted answer

"My question is what is the importance/effect of amino acid A occuring at position I in the sequence with respect to the model?"

I suggest [Monotony and Surprise](http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.65.4858&rep=rep1&type=pdf) by Apostolico for the modeling of importance of words appearing at certain positions, or in certain patterns. Beyond that, I'm not sure what you're looking for.

> **Comments:**
> **username_4**: This link is behind a paywall I think, but is a less technical explanation of the approach.  http://www.springerlink.com/content/nn13140321803528/fulltext.pdf  

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