<p>Sure, so you start out with what is called a bitscore, which is a normalized to the score calculated from the alignment between the 2 seqs which depends on the following equation. It is <strong>independent</strong> of database size:</p>

<blockquote>
  <p>(lambda * S - ln(k))/(ln)2</p>
</blockquote>

<p>Then, the p-value of a local blast is just:</p>

<blockquote>
  <p>1/2^bitscore</p>
</blockquote>

<p>So if your bitscore is 15, you need 1/32768 alignments before you will get a score as good or better (highly similar sequences) <strong>BY CHANCE ALONE</strong>. This addresses your "BY CHANCE" question.</p>

<p>Earlier I said the bitscore was <strong>independent</strong> of database size. The E value is just the p-value above normalized to the database size (so it is <strong>dependent</strong> on the db size) by the following equation:</p>

<blockquote>
  <p>(query length * database length * p-value)</p>
</blockquote>

<p>which simplifies a bit to:</p>

<blockquote>
  <p>E = (query length* (db length/2^bitscore)</p>
</blockquote>

<p>I hope this helps! </p>

CC BY-SA 4.0
2019-02-15T15:41:27.047Z
2019-02-15T19:48:51.473Z
2019-02-15T19:48:51.473Z
d_kennetz
<p>The Blast E is the expected frequency of obtaining false positive. This will depend on your query size (number of nucleotide or amino acid residues) and the size of the database. With a short query and a large database you are more likely to have a sequence in your database that matches your query by simple chance. In summary, the smaller the query and the larger the database the greater the chance of a spurious result and that is what E is measuring.</p>

CC BY-SA 4.0
2019-02-15T12:22:40.293Z
2019-02-18T09:18:08.300Z
2019-02-18T09:18:08.300Z
Pallie
<p>Calculation of E for Blast is a good question. </p>

<p>Two methods:</p>

<ul>
<li>Use a Poison or binomial distribution.</li>
<li>Use randomization</li>
</ul>

<p>I think its no. 1 because no. 2 would use too much computational power.  I did know but someone borrowed by O'Reilly book on the subject.</p>

<p>One of the contributors here will know, because I suspect their genomics developers.</p>

CC BY-SA 4.0
2019-02-14T22:21:20.533Z
2019-02-15T12:03:35.940Z
2019-02-15T12:03:35.940Z
M__
<p>So if you see the BLAST parameters it says </p>

<blockquote>
  <p>The Expected value E  is a parameter that describes the number of hits one can "expect" to get by chance when searching a database of particular size. It decreases exponentially as the score (S) increases. Essential, the E value describes the randomness background noise. For example an E value of 1 assigned to a hit can be interpreted as meaning that a database of the current size one might expect to see 1 match with a similar score simply by chance. Lower the E value the better." </p>
</blockquote>

<p>How could there be something "BY CHANCE" it's a software right ?</p>

<blast>
Randomness in BLAST
# Randomness in BLAST

(Asked by: username_0 on 2019-02-14)

So if you see the BLAST parameters it says

> The Expected value E is a parameter that describes the number of hits one can "expect" to get by chance when searching a database of particular size. It decreases exponentially as the score (S) increases. Essential, the E value describes the randomness background noise. For example an E value of 1 assigned to a hit can be interpreted as meaning that a database of the current size one might expect to see 1 match with a similar score simply by chance. Lower the E value the better."

How could there be something "BY CHANCE" it's a software right ?

**Tags:** blast

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## 3 answers

### Answer by username_2 on 2019-02-15. Score: 7

The Blast E is the expected frequency of obtaining false positive. This will depend on your query size (number of nucleotide or amino acid residues) and the size of the database. With a short query and a large database you are more likely to have a sequence in your database that matches your query by simple chance. In summary, the smaller the query and the larger the database the greater the chance of a spurious result and that is what E is measuring.


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### Answer by username_1 on 2019-02-15. Score: 5

Sure, so you start out with what is called a bitscore, which is a normalized to the score calculated from the alignment between the 2 seqs which depends on the following equation. It is **independent** of database size:

> (lambda \* S - ln(k))/(ln)2

Then, the p-value of a local blast is just:

> 1/2^bitscore

So if your bitscore is 15, you need 1/32768 alignments before you will get a score as good or better (highly similar sequences) **BY CHANCE ALONE**. This addresses your "BY CHANCE" question.

Earlier I said the bitscore was **independent** of database size. The E value is just the p-value above normalized to the database size (so it is **dependent** on the db size) by the following equation:

> (query length \* database length \* p-value)

which simplifies a bit to:

> E = (query length\* (db length/2^bitscore)

I hope this helps!


---

### Answer by username_3 on 2019-02-14. Score: 0

Calculation of E for Blast is a good question.

Two methods:

* Use a Poison or binomial distribution.
* Use randomization

I think its no. 1 because no. 2 would use too much computational power. I did know but someone borrowed by O'Reilly book on the subject.

One of the contributors here will know, because I suspect their genomics developers.


---

