E Value Calculator

The E-value, or expectation value, plays a crucial role in bioinformatics, particularly in the BLAST (Basic Local Alignment Search Tool) algorithm for comparing nucleotide or protein sequences. It provides a statistical measure of the number of times one can expect to find a given sequence alignment by chance in a database of a specified size.

Historical Background

E-value originated from the field of bioinformatics as a fundamental component of sequence alignment tools. It is particularly associated with the BLAST algorithm, developed in the early 1990s, which revolutionized the way researchers could identify similarities between biological sequences.

Calculation Formula

The formula to calculate an E-value in BLAST is as follows:

\[ E = m \times n \times 2^S \]

where:

• \(E\) is the E-value,
• \(m\) is the length of the query sequence,
• \(n\) is the total length of all template sequences in the database,
• \(S\) is the bit score.

Example Calculation

Suppose you have a query sequence of length 300, a total length of all template sequences in the database of 2,000,000, and a bit score of 50. The E-value is calculated as:

\[ E = 300 \times 2,000,000 \times 2^{50} \approx 3.3 \times 10^{20} \]

Importance and Usage Scenarios

In bioinformatics, the E-value helps determine the significance of sequence alignment. A lower E-value indicates a higher significance of the match, helping researchers identify biologically relevant similarities. It is widely used in genomics, proteomics, and evolutionary biology studies.

Common FAQs

1. What does a low E-value indicate?

   • A low E-value suggests that the observed sequence alignment is less likely to have occurred by chance, implying a significant biological relationship.

2. How is the E-value different from the p-value?

   • While both are statistical measures, the E-value specifically refers to the expected number of chance alignments in BLAST searches, whereas the p-value measures the probability of an observed (or more extreme) result assuming the null hypothesis is true.

3. Can E-values predict functional relationships?

   • While E-values can indicate sequence similarity, further analysis is often required to confirm functional relationships due to the complexity of biological systems.

This calculator streamlines the process of calculating E-values, facilitating research in bioinformatics and molecular biology.