BLAST E-value Calculator

An E-value (Expectation value) is an estimate of the expected number of random alignments with a particular score or better that could be found by chance in a given database search. It represents the likelihood that a sequence alignment is due to chance rather than a true biological relationship.

E-values near zero (e.g., 1e-10) indicate highly significant matches unlikely to occur by chance. E-values near 1 or greater suggest the alignment may be due to chance. Generally, E-values < 0.01 are considered significant, while E-values > 1 are not significant.

E-values are calculated using the Karlin-Altschul formula: E = K × m × n × e^(-λS), where K and λ are statistical parameters, m is query length, n is database size (or subject length), and S is the raw alignment score.

E-values depend on database size and search parameters, making them context-dependent. Bit scores are database-independent normalized scores that allow comparison across different searches. Higher bit scores indicate better alignments, while lower E-values indicate better alignments.

E-values increase proportionally with database size because larger databases provide more opportunities for chance alignments. The same alignment will have a higher E-value when searched against a larger database, even though the biological significance remains the same.

For protein searches with BLOSUM62 matrix, typical values are λ ≈ 0.267 and K ≈ 0.041. For nucleotide searches, λ ≈ 1.28 and K ≈ 0.46. These parameters depend on the scoring matrix and gap penalties used.

To increase sensitivity, use lower E-value thresholds (e.g., 10 instead of 0.01), adjust scoring matrices for more distant relationships, use composition-based statistics, or consider using more sensitive algorithms like PSI-BLAST for protein searches.