Answers.Body: <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>
  
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Answers.Body: <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>
  
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Answers.UserDisplayName: Pallie
Answers.Body: <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>
  
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Body: <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>
  
Tags: <blast>
Title: Randomness in BLAST
ThreadText: # 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
  
  
  ---
  
  ## 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.
  
  
  ---
  
  ### 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.
  
  
  ---
  
  