When performing a blast search, researchers are often interested in finding similarities between a query sequence and a large database of sequences. Blast search stands for Basic Local Alignment Search Tool and it is widely used in bioinformatics to compare biological sequences such as DNA, RNA, and proteins. One of the key factors in blast search results is the E-value.
The E-value in blast search is a statistical measure of the expected number of random matches that could occur by chance when comparing a query sequence against a database. It represents the probability of obtaining a match as good or better than the one observed, purely by chance.
Typically, lower E-values indicate more significant matches, suggesting a higher likelihood that the observed similarity between the query and a sequence in the database is due to actual biological relationships rather than random chance.
FAQs about E-value in blast search:
1. How is the E-value calculated in a blast search?
The E-value is calculated based on the size of the database being searched, the length of the query sequence, and the quality of the matches found.
2. Can the E-value be zero?
No, the E-value cannot be zero. A value close to zero indicates a highly significant match.
3. Is a lower E-value always better?
Yes, a lower E-value indicates a more significant match. However, the biological relevance of the match should also be considered.
4. How is the E-value interpreted?
The E-value can be interpreted as the number of matches you would expect to find by chance in the database of sequences if no significant similarity exists.
5. What is the significance threshold for E-values?
The significance threshold for E-values commonly used in bioinformatics is 0.01. Matches with E-values below this threshold are considered statistically significant.
6. Can E-values be negative?
No, E-values cannot be negative.
7. How can E-values help in identifying homologous sequences?
E-values help in identifying homologous sequences by providing an estimate of the probability that the match between the query sequence and a database sequence is due to random chance.
8. Are E-values affected by the size of the database being searched?
Yes, larger databases tend to have higher E-values because the probability of finding random matches increases with more sequences.
9. How can I determine if an E-value is significant?
Generally, E-values smaller than 0.01 are considered statistically significant, but the significance depends on the specific context of the analysis and the desired level of stringency.
10. Can different blast programs produce different E-values for the same query?
Yes, different blast programs may use different algorithms and scoring schemes, which can lead to variations in E-values for the same query.
11. Are E-values affected by the length of the query sequence?
Yes, longer query sequences tend to have lower E-values because longer sequences have a higher chance of generating a significant match.
12. How can I optimize my blast search to get better E-values?
Optimizing blast search can involve adjusting parameters such as word size, gap penalties, and substitution matrices to improve the probability of finding significant matches and obtaining lower E-values.
In conclusion, the E-value in blast search is a crucial statistical measure that helps researchers determine the significance of the matches found between a query sequence and a database. By considering the E-value, researchers can assess the likelihood of a match being due to chance or an actual biological relationship, aiding in the interpretation and analysis of blast search results.