<p>This is explained in <a href="https://www.ncbi.nlm.nih.gov/pubmed/2172928" rel="nofollow noreferrer">the original paper</a> [1] describing the logos (emphasis mine):</p>

<blockquote>
  <p>The importance of a particular position in a binding site is more clearly
  and consistently given by the information required to describe the pattern
  there [7, 8]. To choose one symbol or state from two equally likely possibilities
  requires one "bit" of information. For example, to communicate the result of
  a coin-ip to someone requires 1 bit of information because only one yes-no
  question needs to be answered: "Is it heads?". <strong>If a position in a binding
  site always contains one base (e.g. G), then we need exactly two bits of
  information since two yes-no questions need to be answered: "Is it A or G?"
  (i.e. is it a purine?) and "Is it A or C?". (If the answers to both questions
  are "no", it must be a T.)</strong> Furthermore, if a position contains two bases (e.g.
  sometimes A and sometimes G), only one question suffices since a two out of
  four choice is equivalent to a one out of two choice. Therefore, only one bit
  is needed to describe a position in a binding site that contains only purines,
  but two bits are needed to describe a position that always contains adenine.</p>
</blockquote>

<p>So yes, 2bits is the highest value you will see on the y-axis of a <strong><em>DNA</em></strong> sequence logo (proteins are a different story since there are more possibilities). In the one you show, the scale is from 0 to 0.2, but it's the same principle. </p>

<p>However, you should think of logos as a useful visual aid, and not a way of getting rigorous mathematical information about a sequence. So don't put too much weight on the bit values. If you need that sort of data, calculate it from the alignment directly. </p>

<hr>

<p>[1] Schneider TD, Stephens RM., Sequence logos: a new way to display consensus sequences., <em>Nucleic Acids Res.</em> 1990 Oct 25;18(<strong>20</strong>):6097-100.</p>

CC BY-SA 4.0
2019-08-01T09:38:33.093Z
2019-08-01T09:38:33.093Z
terdon
<p>In bioinformatics, a <a href="https://en.wikipedia.org/wiki/Sequence_logo" rel="nofollow noreferrer">sequence logo</a> is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences).</p>

<p>wiki says</p>

<blockquote>
  <p>The total height of the letters depicts the information content of the
  position, in bits.</p>
</blockquote>

<p>and then gives this example</p>

<blockquote>
  <p>A sequence logo showing the most conserved bases around the initiation
  codon from all human mRNAs (Kozak consensus sequence). Note that the
  initiation codon is not drawn to scale, otherwise the letters AUG
  would each have a height of 2 bits.</p>
</blockquote>

<p><a href="https://i.sstatic.net/eA1L0.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/eA1L0.png" alt="e"></a></p>

<p>it seems that there is a 0.1 bit letter.</p>

<p>is this in the context of 2bits? is 2bits the highest bits in this sequence logo? Is there a convention or standard of the highest bits in a sequence logo?</p>

CC BY-SA 4.0
2019-08-01T09:24:57.187Z
Sequence logos are usually just visual aids, why do you need the bits? I mean, if you want to get numbers representing the frequency of a residue at a given position, then logos are probably not the right approach.
terdon
<ngs><sequence-analysis>
Is there a convention or standard of the highest bits in a sequence logo?
# Is there a convention or standard of the highest bits in a sequence logo?

(Asked by: username_0 on 2019-08-01)

In bioinformatics, a [sequence logo](https://en.wikipedia.org/wiki/Sequence_logo) is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences).

wiki says

> The total height of the letters depicts the information content of the
> position, in bits.

and then gives this example

> A sequence logo showing the most conserved bases around the initiation
> codon from all human mRNAs (Kozak consensus sequence). Note that the
> initiation codon is not drawn to scale, otherwise the letters AUG
> would each have a height of 2 bits.

[![e](https://i.sstatic.net/eA1L0.png)](https://i.sstatic.net/eA1L0.png)

it seems that there is a 0.1 bit letter.

is this in the context of 2bits? is 2bits the highest bits in this sequence logo? Is there a convention or standard of the highest bits in a sequence logo?

**Tags:** ngs, sequence-analysis
> **Comments:**
> **username_1**: Sequence logos are usually just visual aids, why do you need the bits? I mean, if you want to get numbers representing the frequency of a residue at a given position, then logos are probably not the right approach.  

---

## 1 answers

### Answer by username_1 on 2019-08-01. Score: 1 | Accepted answer

This is explained in [the original paper](https://www.ncbi.nlm.nih.gov/pubmed/2172928) [1] describing the logos (emphasis mine):

> The importance of a particular position in a binding site is more clearly
> and consistently given by the information required to describe the pattern
> there [7, 8]. To choose one symbol or state from two equally likely possibilities
> requires one "bit" of information. For example, to communicate the result of
> a coin-ip to someone requires 1 bit of information because only one yes-no
> question needs to be answered: "Is it heads?". **If a position in a binding
> site always contains one base (e.g. G), then we need exactly two bits of
> information since two yes-no questions need to be answered: "Is it A or G?"
> (i.e. is it a purine?) and "Is it A or C?". (If the answers to both questions
> are "no", it must be a T.)** Furthermore, if a position contains two bases (e.g.
> sometimes A and sometimes G), only one question suffices since a two out of
> four choice is equivalent to a one out of two choice. Therefore, only one bit
> is needed to describe a position in a binding site that contains only purines,
> but two bits are needed to describe a position that always contains adenine.

So yes, 2bits is the highest value you will see on the y-axis of a ***DNA*** sequence logo (proteins are a different story since there are more possibilities). In the one you show, the scale is from 0 to 0.2, but it's the same principle.

However, you should think of logos as a useful visual aid, and not a way of getting rigorous mathematical information about a sequence. So don't put too much weight on the bit values. If you need that sort of data, calculate it from the alignment directly.

---

[1] Schneider TD, Stephens RM., Sequence logos: a new way to display consensus sequences., *Nucleic Acids Res.* 1990 Oct 25;18(**20**):6097-100.


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