<p>Protein autocorrelation is similar to usual autocorrelation of time series (that is, function <span class="math-container">$r(k)$</span> measuring correlation between values lagged by <span class="math-container">$k$</span>), except that instead of time dimension we slide along the backbone of amino acid chain. The "dependent variable" can be any quantifiable property of the amino acids - then the autocorrelation measures similarity in that particular property.</p>

<p>See e.g. Fernandez et al., 2008, for more extensive background:
<a href="https://www.tandfonline.com/doi/full/10.1080/08927020802301920?scroll=top&amp;needAccess=true" rel="nofollow noreferrer">https://www.tandfonline.com/doi/full/10.1080/08927020802301920?scroll=top&amp;needAccess=true</a></p>

CC BY-SA 4.0
2018-09-24T23:31:52.363Z
2018-09-24T23:31:52.363Z
juod
<p>Given a normal protein sequence with the 20 standard amino acids, how can the 'Autocovariances', 'autocorrelations', and 'autocorrelation coefficients' of the sequence be calculated?</p>

<p>What is meant by these terms in the context of a protein sequence?</p>

<p>What are the appropriate algorithms and formulas?</p>

<p>Is there any existing package/function to calculate these values?</p>

CC BY-SA 4.0
2018-09-24T14:28:46.723Z
Could you provide some context? It could clarify the question and attract more answers. Maybe you read that in an article or it is for some specific goal in mind, or someone asked you this because a discussion about another topic
llrs
<proteins><r><features>
How can the Autocovariances, autocorrelations, and autocorrelation coefficients be calculated from a Protein Amino Acid Sequence?
# How can the Autocovariances, autocorrelations, and autocorrelation coefficients be calculated from a Protein Amino Acid Sequence?

(Asked by: username_0 on 2018-09-22)

Given a normal protein sequence with the 20 standard amino acids, how can the 'Autocovariances', 'autocorrelations', and 'autocorrelation coefficients' of the sequence be calculated?

What is meant by these terms in the context of a protein sequence?

What are the appropriate algorithms and formulas?

Is there any existing package/function to calculate these values?

**Tags:** proteins, r, features
> **Comments:**
> **username_1**: Could you provide some context? It could clarify the question and attract more answers. Maybe you read that in an article or it is for some specific goal in mind, or someone asked you this because a discussion about another topic  

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## 1 answers

### Answer by username_2 on 2018-09-24. Score: 2 | Accepted answer

Protein autocorrelation is similar to usual autocorrelation of time series (that is, function $r(k)$ measuring correlation between values lagged by $k$), except that instead of time dimension we slide along the backbone of amino acid chain. The "dependent variable" can be any quantifiable property of the amino acids - then the autocorrelation measures similarity in that particular property.

See e.g. Fernandez et al., 2008, for more extensive background:
<https://www.tandfonline.com/doi/full/10.1080/08927020802301920?scroll=top&needAccess=true>


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