Sequence Alignment and Reading a Search Result · seed 1 · A4, ink-friendly. The answer key prints on its own page for grown-ups.

Scoring alignments and judging hits

Science · Genetics & Evolution · ages 20-22
Name ______________________   Date ____________

  1. What does the reported statistic on a hit tell you?

    • How often such a match would appear by chance
    • The age of the database
    • The name of the sequencer

  2. How is the best alignment chosen?

    • The longest one always wins
    • The highest total score wins
    • The one with most gaps wins

  3. Why does a short query give weak statistics even when perfect?

    • Short machines run slowly
    • Few letters can match by luck
    • Short queries are always wrong

  4. Hit A has a high score and a tiny chance value. Hit B has a similar score but a large chance value. Which is strong?

    • Hit A, because chance cannot explain it
    • Hit B, because large values impress
    • Both equally, scores match

  5. Scheme: +2 match, -1 mismatch, -2 gap. An alignment has 3 matches and 1 gap. Give the total.

    Answer: ______________

  6. Under +2/-1/-2, an alignment with 2 matches and 1 mismatch scores 3.

    Circle one:   True   False

  7. Two alignments of the same pair score 4 and 1 under one scheme. A friend picks the 1. What is wrong?

    • Nothing, lower is better
    • Scores cannot be compared at all
    • The best alignment is the highest total, so 4 wins

  8. A student trusts a short perfect hit with a weak statistic. What is the error?

    • Weak statistics still warn that luck explains it
    • Perfect matches need no statistics
    • Databases never hold short sequences
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Answer key

For grown-ups. Fold this page away before handing over the rest.

Scoring alignments and judging hits W1-mt_jNbEMFqgZ5-s1

  1. How often such a match would appear by chance · It separates meaningful similarity from lucky similarity.
  2. The highest total score wins · Matches, mismatches, and gaps sum to a total, and the top total wins.
  3. Few letters can match by luck · Chance matches are easy with few letters, so the math stays cautious.
  4. Hit A, because chance cannot explain it · The statistic breaks the tie: tiny chance means real similarity.
  5. 4 · Three matches give 6, one gap costs 2, and 6 minus 2 is 4.
  6. True · Two matches give 4, one mismatch costs 1, leaving 3.
  7. The best alignment is the highest total, so 4 wins · Best means highest total under the stated scheme.
  8. Weak statistics still warn that luck explains it · The statistic already accounts for length; weak means unconvincing.
Worksheet · LightMySky