Topic 2 - Pairwise Sequence Alignment

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Last updated 4:14 AM on 10/11/26
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30 Terms

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What is sequence homology?
Shared evolutionary ancestry; homology is qualitative, not a percentage.
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What is sequence similarity?
A measurable degree of resemblance between two sequences.
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What are orthologs?
Homologous genes that diverged through speciation.
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What are paralogs?
Homologous genes that diverged through gene duplication.
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What is sequence identity?
The fraction or percentage of aligned positions with identical residues.
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What is global alignment?
Aligns two sequences over their entire lengths; Needleman-Wunsch.
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When is global alignment useful?
When sequences are similar across most of their lengths.
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What is semi-global alignment?
An alignment that does not penalize specified terminal gaps; modified Needleman-Wunsch.
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When is semi-global alignment useful?
When sequences overlap or differ at their ends.
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What is local alignment?
Finds the highest-scoring related region; Smith-Waterman.
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When is local alignment useful?
When sequences share only an isolated similar region.
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What is dynamic programming (DP)?
Solving smaller alignment subproblems and storing optimal scores in a matrix.
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What are the main DP alignment steps?
Initialize matrix; fill scores and arrows; traceback; write optimal alignment.
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What does a diagonal DP move mean?
Align two residues as a match or mismatch.
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What do horizontal and vertical DP moves mean?
Align a residue with a gap.
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What is a gap penalty?
A score penalty for introducing gaps into an alignment.
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What is a linear gap penalty?
The same penalty is applied for each gap position.
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What is an affine gap penalty?
A separate cost for opening a gap and for extending it.
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What is the global DP recurrence?
F(i,j)=max[diagonal+substitution score, up+gap score, left+gap score].
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What is the local DP recurrence?
F(i,j)=max[0, diagonal+substitution score, up+gap score, left+gap score].
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Why does local DP include zero?
To stop negative-scoring alignments and allow new local alignments to start.
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How is the global DP matrix initialized with gap score g?
F(0,0)=0; first row and column accumulate gap penalties.
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How is the local DP matrix initialized?
The first row and first column are all zero.
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Where does global traceback start and end?
Starts at bottom right and ends at top left.
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Where does local traceback start and end?
Starts at the maximum cell and ends when it reaches zero.
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Where does semi-global traceback start?
At the best allowed terminal cell, often the maximum in the last row or last column, depending on free-end-gap rules.
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Where does semi-global traceback end?
At the first row or column corresponding to a free terminal gap.
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Where is the global alignment score found?
The bottom-right DP cell.
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Where is the local alignment score found?
The maximum value anywhere in the DP matrix.
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Can an alignment have more than one optimal traceback?
Yes; tied choices can produce different alignments with the same optimal score.