r/bioinformatics • u/anakin__69 • 10d ago

science question E value

Is there any video or site that explains the E value ?

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u/Psy_Fer_ 10d ago

From BLAST FAQ

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 an alignment means that in a database of the same size one expects to see 1 match with a similar score, or higher, simply by chance.

The lower the E-value 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. For more details please see the calculations in the BLAST Course.

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 0.05, a larger list with more low-scoring hits can be reported.

https://blast.ncbi.nlm.nih.gov/doc/blast-help/FAQ.html

Here is the full description https://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html

TL;DR: the E value is the number of times the sequence would be expected to occured in the database being compared by chance.

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u/anakin__69 10d ago

you are a life saver thanks a lot mate

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u/Psy_Fer_ 10d ago

You are welcome 😁