Metagenomics - E-value & Bit-score (2024)

FAQs

Metagenomics - E-value & Bit-score? ›

The E-value (expectation value) is a corrected bit-score adjusted to the sequence database

Bit score is a normalized score and hence it is independent of the size of the database, while E- values are very sensitive to the database size. Generally, bit scores of 40 or higher are considered reliable.

If E is between 0.01 and 1e - 50, the match can be considered a result of hom*ology. If E is between 0.01 and 10, the match is considered not significant, but may hint at a tentative remote hom*ology relationship. Additional evidence is needed to confirm the tentative relationship.

In addition to the bitscore, an e-value is reported for each BLAST hit. This value indicates whether this hit may be due to chance, rather than a real similarity between query and hit sequence. The e-value is based on the bitscore, but is transformed according to the sizes of the query and the database.

Lower (i.e., stronger) E-values indicate more significant alignments, suggesting a higher probability that the sequences share a common evolutionary origin. A higher (i.e., weaker) E-value indicates that the alignment might be a random event.

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.

Bit score is an important measure that gives an indication about the statistical significance of an alignment. In simple terms, the higher the bit score, the more similar the two sequences are. Bit scores below 50 are generally assumed to be untrustworthy.

In principle E-value lower than 0.05 can be considered as a statistically significant hit. However, in practice one consider even more stringent E-value cut-offs. A hit may have very low E-value but still can be a false positive.

The e-value is basically a measure of how many such alignments you would expect to find in a database this size by chance. Therefore, e-values greater than 1 mean that you'd expect at least one alignment similar to what you've found by chance alone.

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...

Is an E-value of 0 good? ›

An e-value of 0.0 means zero sequences can/are expected to match as well or better; the closer the e-value is to zero, the more significant (and less of a potential false positive) the match is considered to be.

E-value: Indicates the number of hits or alignments that are expected to be seen by random chance with the same score or better. The lower the E-value, the more significant the alignment (the closer to 0, the better).

Within a database of a particular size, "E-value" is the number of results that may come up. If you get an E-value of 3 or less than you have a very good chance that the match is meaningful and not due to random chance.

If the value of E°_cell is positive, the reaction will occur spontaneously as written. If the value of E°_cell is negative, then the reaction is not spontaneous, and it will not occur as written under standard conditions; it will, however, proceed spontaneously in the opposite direction.

BLAST results do not typically attempt to match the full length of a sequence. A high Query Cover value for the initial triage is in the 70%+ range. If the top results fall below this range, it would generally be a good idea to review the sequence more in the future, and not verify it as a part of your initial triage.

The list of hits starts with the best match (most similar). E-value: expected number of chance alignments; the smaller the E-value, the better the match. First in the list is the query sequence itself, which obviously has the best score.

The E-value is directly proportional to the database size. Note: Conceptually this is easy to understand - getting an alignment with the given score (205 bits) is more SIGNIFICANT in the smaller database. In larger database there is a larger chance of randomly picking up matches.

The bit-score (S) is determined by the following formula: S = (λ × S − lnK)/ ln2 where λ is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix.

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).

The relevant statistic is called the Expect Value or e-value. Expect value — for a particular match, the number of chance alignments expected with the same score or a better one. The Expect value is an exponentially decreasing function of the score and is directly proportional to the search space.