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. … These high E values make sense because shorter sequences have a higher probability of occurring in the database purely by chance.
What is a good e value?
Blast hits with E-value
smaller than 0.01
can still be considered as good hit for homology matches. E-value smaller than 10 will include hits that cannot be considered as significant, but may give an idea of potential relations.
Is a high E value good?
The e-value represents the expectation of finding that sequence by random chance. So if you search a short sequence you are likely to have
a lot more hits
with high e-value (low significance), and if you search a long sequence you are likely to have fewer hits with lower e-value (greater significance).
What is a good percent identity in blast?
The BLAST nucleotide sequence identity suggested
75-98%
relationship or similarity, depending on the fungi type.
What does an E value of 0 mean?
the e value give a measure of the similarity of sequences, the lower the e value, the higher the congruity of your query sequence and the retrieved sequence. e values of 0 mean
that there’s an exact match for you sequence here
… mike.
What is the E value on blast?
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
.
What does an E value of 0.05 mean?
For example, an alignment obtaining an E-value of 0.05 means that
there is a 5 in 100 chance of occurring by chance alone
. E-values are very dependent on the query sequence length and the database size. Short identical sequence may have a high E-value and may be regarded as “false positive” hits.
What is the E value cut off?
What e-value do you use as a cutoff (and for what purpose) when you are computing a BLAST? Users mainly used the e-value as a cutoff to define a Blast “hit”. However depending on what they do this cut-off change From
1e-2 to 1e-30
!
What is E value in pharmacy?
The relationship between the amount of drug that produces a particular osmolarity and the amount of sodium chloride that produces the same osmolarity is called the
sodium chloride equivalent
, which many people call the “E value” for short.
What is the difference between e value and p value?
A p-value is the
probability of making a
mistake. An E-value is the expected number of times that the given score would appear in a random database of the given size.
What is the max score on BLAST?
Max[imum] Score: the highest alignment
score calculated from the sum of the rewards for
matched nucleotides or amino acids and penalities for mismatches and gaps. Tot[al] Score: the sum of alignment scores of all segments from the same subject sequence.
What does positives mean in BLAST?
Positives. In the context of alignments displayed in BLAST output, positives are those
non-identical substitutions that receive a positive score in the underlying scoring matrix
, BLOSUM62 by default. Most often, positives indicate a conservative substitution or substitutions that are often observed in related proteins.
What do BLAST results mean?
BLAST uses statistical theory to produce a bit score
and expect value
(E-value) for each alignment pair (query to hit). The bit score gives an indication of how good the alignment is; the higher the score, the better the alignment.
Can an e value be 0?
Very low e-values are rounded to zero
. BLAST uses double float point representation, so e-values lower than approximately 5*10^−324 are rounded to 0.
What does a negative e value mean?
The Ecell value is obtained from the two half reactions or the balanced chemical equation. Ecell is
E(cathode) minus E(anode)
. For deltaG to be negative, which indicates that the reaction is a spontaneous one, E cell must be positive.
What is p value in blast?
p value.
The probability of a chance alignment occurring with a particular score or a better score
in a database search.
