145. Of the two databases A and B, the database A is larger in size than database B. In a BLAST search, a
sequence has a highly significant match with the same entry in both the databases. Which of the following is
TRUE?
1. Match in Database A will have lower E-value when compared to Database B
2. Match in Database B will have lower E-value when compared to Database A
3. The E-value will be same for both the matches
4. The E-value cannot be compared for such a search

Question

Of the two databases A and B, the database A is larger in size than database B. In a BLAST search, a sequence has a highly significant match with the same entry in both the databases. Which of the following is TRUE?

1. Match in Database A will have lower E-value when compared to Database B

2. Match in Database B will have lower E-value when compared to Database A

3. The E-value will be same for both the matches

4. The E-value cannot be compared for such a search

Detailed Explanation

In bioinformatics, BLAST (Basic Local Alignment Search Tool) is a widely used tool to find similarities between biological sequences, such as DNA, RNA, or protein sequences. The E-value (Expect value) is a parameter used in sequence alignment to measure the number of matches one can expect to see by chance in a database search. A lower E-value indicates a more significant match.

When performing a BLAST search, the E-value depends on several factors, including:

• The size of the database: Larger databases tend to have more sequences, which increases the likelihood of finding a match by chance.

• The length of the query sequence: Longer sequences are more likely to find significant matches.

• The alignment score: Higher scores generally lead to lower E-values.

Effect of Database Size on E-value

When comparing two databases of different sizes, database A (larger) and database B (smaller), the size of the database impacts the E-value:

• In database A, because it is larger, there is a higher chance of finding a match by random chance. As a result, for the same alignment, the E-value will be higher for database A compared to database B.

• In database B, being smaller, the likelihood of a random match is lower, which leads to a lower E-value for the same match when compared to the larger database A.

This is because a smaller database reduces the number of potential alignments that could happen by chance, making a real match appear more significant (lower E-value). Conversely, in a larger database, the probability of a random match increases, resulting in a higher E-value.

Answering the Question

The correct answer is:

2. Match in Database B will have lower E-value when compared to Database A

This is because the smaller database (B) has fewer sequences, so the likelihood of finding a random match is reduced, resulting in a more significant match (lower E-value) compared to the larger database (A).

Conclusion

In BLAST searches, the size of the database plays a crucial role in determining the E-value. For a highly significant match found in both databases A (larger) and B (smaller), the match in the smaller database (B) will have a lower E-value than in the larger database (A). This is due to the increased likelihood of finding a random match in a larger database.