A BLAST hit has E = 2. What does that value mean?

• Two chance alignments at least this strong are expected
• The hit has exactly a two-percent probability of being false
• Two biological functions have been confirmed for the hit

For candidate alignments using the same scoring scheme and constraints, which rule selects the best score?

• Choose the longest alignment regardless of penalties
• Choose the alignment with the highest total score
• Choose the alignment with the most gap characters

Why can a short query have a large E-value even when its aligned letters match perfectly?

• Perfect identity makes database size irrelevant
• A short sequence can also occur by chance
• Every perfect short match contains a sequencing error

In one BLAST search, hit A has E = 0.000001 and hit B has E = 2. Which statement follows from these values?

• Hit B has stronger support because its E-value is larger
• Hit A's exact function is now experimentally established
• Hit A has stronger evidence against a chance match

Use +2 per match, -1 per mismatch and -2 per gap character. An alignment has 5 matches, 2 mismatches and 1 gap character. What is its total score?

With +2 per match, -1 per mismatch and -2 per gap character, an alignment with 2 matches, 1 mismatch and no gaps scores 3.

Use +2 per match, -1 per mismatch and -2 per gap character. For 4 matches, 2 mismatches and 1 gap, a friend writes 8 + 2 = 10 and stops. What repairs the calculation?

• Add every penalty as positive and leave the gap unscored
• Use 8 - 2 and omit the penalty for the gap character
• Use 8 - 2 - 2 = 4, subtracting both penalties

A long query has a tiny E-value for an alignment covering only a short region. A student assigns the hit's full protein function to the query. What is still needed?

• Evidence that the matched region supports that function
• A rule that any tiny E-value proves the full protein function
• A larger E-value before any biological evidence is considered