text: user4131: 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 ?
  
  user3669: 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! 
  
  user3818: 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.
  
original_text: 4131: <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>
   3669: <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>
   3818: <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>
  