Expect value: Difference between revisions

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 The Expect value (E) is a parameter that describes the number of hits one can "expect" to see by chance when searching a database of a particular size. It decreases exponentially as the Score (S) of the match increases. Essentially, the E value describes the random background noise. For example, an E value of 1 assigned to a hit can be interpreted as meaning that in a database of the current size one might expect to see 1 match with a similar score simply by chance.  
The Expect Value (E) is the number of hits that a person would expect by chance when searching a [[Database|database]]. The lower this value is, the higher the [[Score (S) - BLAST|Score (S)]] of the match is. The closer the E-value gets to zero, the better the match is. You can increase or decrease it, depending on how small your sequences are, for example, if you are searching smaller sequences, you could increase the E value from 10 to 1000.  


The lower the E-value, or the closer it is to zero, the more "significant" the match is. However, keep in mind that virtually identical short alignments have relatively high E values. This is because the calculation of the E value takes into account the length of the query sequence. These high E values make sense because shorter sequences have a higher probability of occurring in the database purely by chance.  
The lower the E-value, or the closer it is to zero, the more "significant" the match is. But another factor that affects the E-value is the length of the query. Since shorter ones have a higher chance of occurring in the database, they tend to have a higher E-value<ref>National Library of Medicine, BLAST Frequently Asked Questions [online], available at: http://www.ncbi.nlm.nih.gov/blast/ef&amp;gt;. fckLRfckLR=== References  ===fckLRfckLR&amp;lt;references /&amp;gt;</ref>.  


The Expect value can also be used as a convenient way to create a significance threshold for reporting results. You can change the Expect value threshold on most BLAST search pages. When the Expect value is increased from the default value of 10, a larger list with more low-scoring hits can be reported.<ref>National Library of Medicine, BLAST Frequently Asked Questions [online], available at: &amp;amp;amp;amp;amp;amp;lt;http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&amp;amp;amp;amp;amp;amp;amp;PAGE_TYPE=BlastDocs&amp;amp;amp;amp;amp;amp;amp;DOC_TYPE=FAQ#expect&amp;amp;amp;amp;amp;amp;gt;, [accessed 20/Oct/2013]</ref>
=== References  ===


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<ref>National Library of Medicine, BLAST Frequently Asked Questions [online], available at: &amp;amp;amp;amp;amp;amp;lt;http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&amp;amp;amp;amp;amp;amp;amp;PAGE_TYPE=BlastDocs&amp;amp;amp;amp;amp;amp;amp;DOC_TYPE=FAQ#expect&amp;amp;amp;amp;amp;amp;gt;, [accessed 20/Oct/2013]</ref>

Latest revision as of 06:54, 23 October 2018

The Expect Value (E) is the number of hits that a person would expect by chance when searching a database. The lower this value is, the higher the Score (S) of the match is. The closer the E-value gets to zero, the better the match is. You can increase or decrease it, depending on how small your sequences are, for example, if you are searching smaller sequences, you could increase the E value from 10 to 1000.

The lower the E-value, or the closer it is to zero, the more "significant" the match is. But another factor that affects the E-value is the length of the query. Since shorter ones have a higher chance of occurring in the database, they tend to have a higher E-value[1].

References

  1. ↑ National Library of Medicine, BLAST Frequently Asked Questions [online], available at: http://www.ncbi.nlm.nih.gov/blast/ef&gt;. fckLRfckLR=== References ===fckLRfckLR&lt;references /&gt;
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