BLAST E-value Calculator

BLAST E-value Calculator. The BLAST E-value Calculator computes the Expect value (E-value) for a sequence alignment — the number of hits you'd expect to see by chance when searching a database, used in bioinformatics to judge whether a DNA or protein match is statistically meaningful. Enter your Raw Alignment Score, Query Length, Subject Length, Database Size, and Karlin-Altschul parameters (Lambda and K) to get the E-value and P-value. Secondary outputs include Bit Score, Search Space, and a Significance rating for the alignment. Also try the use the Codon Optimization Calculator.

Raw Alignment Score (S) *

Sum of substitution matrix scores

Query Length (m) *

Length of query sequence

Subject Length (n) *

Average length in database or subject sequence length

Database Size (D) *

Number of sequences in database

Lambda (λ) *

Scaling factor for scoring system (default for BLOSUM62)

K Parameter *

Search space parameter (default for BLOSUM62)

Results

E-value

Bit Score

P-value

Search Space

Significance

What is an E-value?

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. See also our Sequence Identity Calculator.

How do I interpret E-values?

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.

How is the BLAST E-value calculated?

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.

What is the difference between E-value and bit 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.

Why do E-values change with database size?

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.

What are typical Lambda and K parameter values?

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.

How can I improve the sensitivity of my BLAST search?

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.