Entire BME 480: Ex 1

Two sequences have 85% identity. Can we say they are 85% homologous?

No. Homology is shared ancestry, not a percentage.

True or false: Similar sequences must share a common ancestor.

False. Similarity supports but does not prove homology.

Two genes diverged after a species split. Are they orthologs or paralogs?

Orthologs.

Two genes arose through duplication. Are they orthologs or paralogs?

Paralogs.

Two full-length sequences are similar throughout. Which alignment is best?

Global alignment (Needleman-Wunsch).

Only one short region is shared. Which alignment is best?

Local alignment (Smith-Waterman).

One sequence overlaps the end of another. Which alignment is best?

Semi-global alignment.

True or false: Semi-global alignment always penalizes all terminal gaps.

False. Certain terminal gaps are free.

Where does traceback start in global alignment?

Bottom-right cell.

Where does traceback start in local alignment?

The highest-scoring cell anywhere in the matrix.

When does local-alignment traceback stop?

At a cell with score zero.

Why can local alignment never have a negative cell score?

Its recurrence includes zero as an option.

A traceback moves diagonally. What does that mean?

Two residues are aligned: match or mismatch.

A traceback moves horizontally or vertically. What does that mean?

A gap is introduced in one sequence.

True or false: There can be more than one optimal alignment.

True. Tied traceback paths can yield equal scores.

Which penalizes opening a new gap differently from extending one?

Affine gap scoring.

In semi-global alignment, where can the best score occur?

At an allowed endpoint, often the last row or column.

What extra option appears in Smith-Waterman but not Needleman-Wunsch?

Zero.

Why not score all protein substitutions equally?

Some amino acid substitutions are more biologically common than others.

Which matrix uses an explicit evolutionary model: PAM or BLOSUM?

PAM.

Which matrix is built from conserved ungapped blocks?

BLOSUM.

True or false: BLOSUM is derived using ancestral phylogenetic trees.

False.

What does the number in PAM250 describe?

250 PAM1 evolutionary steps.

Which is suited to more divergent sequences: PAM30 or PAM250?

PAM250.

Which is suited to more divergent sequences: BLOSUM80 or BLOSUM45?

BLOSUM45.

True or false: Higher PAM and higher BLOSUM numbers both mean more divergence.

False. Higher PAM means more divergence; higher BLOSUM means a higher identity cutoff.

What does 62 mean in BLOSUM62?

The sequence identity cutoff used for clustering.

A substitution has a positive log-odds score. What does that mean?

It occurs more often than expected by chance.

A substitution has a negative log-odds score. What does that mean?

It occurs less often than expected by chance.

If observed and expected frequencies are equal, what is the log-odds score?

Zero.

What does a diagonal substitution-matrix entry score?

Aligning a residue with itself.

True or false: In a symmetric scoring matrix, S(A,G) = S(G,A).

True.

What is the random-model probability of an ordered pair i,j?

P(i) × P(j).

What is the expected frequency of an unordered pair of different residues?

2 × p(i) × p(j).

Which is a qualitative claim: sequence identity or homology?

Homology.

If a substitution score is high, is that proof of shared ancestry?

No. It means the substitution is favored relative to chance.

Why is BLAST usually faster than running Smith-Waterman on a database?

It uses heuristic seeds and extensions instead of exhaustive alignment.

True or false: BLAST always finds the mathematically optimal local alignment.

False.

Which starts with exact word hits: FASTA or BLAST?

FASTA.

Which can start from similar high-scoring words: FASTA or BLAST?

BLAST.

What happens if FASTA word size increases?

Search generally speeds up but sensitivity decreases.

A BLAST hit has a very low E-value. What does that suggest?

It is unlikely to arise by chance.

Which result is stronger: E = 1e-20 or E = 0.1?

E = 1e-20.

Which result is stronger: bit score 180 or 70?

Bit score 180.

True or false: E-value is the probability that two sequences are homologous.

False. It is the expected number of random hits at least as strong.

What does a high query coverage tell you?

Much of the query sequence is included in the alignment.

What does 90% identity mean?

90% of the aligned positions are identical.

A match covers 5% of a long query with high identity. What should you check?

Query coverage; it may represent only a short shared region.

What does HSP stand for?

High-Scoring Segment Pair.

If the E-value threshold is lowered, what happens to stringency?

It increases.

True or false: Increasing stringency can increase false negatives.

True.

What is a false positive in a homology search?

An unrelated sequence incorrectly reported as a homolog.

What is a false negative in a homology search?

A true homolog missed by the search.

What is BLAST word threshold T used for?

To decide which short word matches qualify as seeds.

What is BLAST drop-off X used for?

To stop extension after the score drops too far.

If the same raw score is searched against a much larger database, what tends to happen to E?

It increases because more random hits are expected.

Which MSA method guarantees the optimal score but is very expensive?

Exact multidimensional dynamic programming.

Which MSA method builds an alignment using a guide tree?

Progressive alignment.

Which MSA method can revisit and improve early decisions?

Iterative alignment.

Which MSA method uses agreement across pairwise alignments?

Consistency-based alignment.

Which MSA method uses known protein 3D structures?

Structure-based alignment.

True or false: Progressive alignment can freely correct all early gap placements.

False.

Why is iterative alignment sometimes more accurate than progressive?

It can revise earlier alignment choices.

You have reliable protein structures. Which MSA approach may help most?

Structure-based alignment.

Which tool is associated with progressive alignment: Clustal or T-Coffee?

Clustal.

Which tool is associated with consistency-based alignment?

T-Coffee.

What does an SP score sum within an MSA column?

Scores of all unique sequence pairs.

How many unique pairs are there among 5 sequences?

5 × 4 / 2 = 10.

What does SPS compare against a reference alignment?

Correctly recovered aligned residue pairs.

What does CS compare against a reference alignment?

Entire correctly reproduced columns.

Which is stricter about exact column agreement: SPS or CS?

CS.

True or false: SPS = 1 means every reference residue pair was recovered.

True.

What does the total height of a sequence-logo stack represent?

Information content at that position.

What determines each letter’s height in a sequence logo?

Its frequency multiplied by the position’s information content.

A logo position has high entropy. Is it highly conserved?

No. High entropy means more variation.

A DNA column contains only A. What are its entropy and information content?

Entropy 0 bits; information content 2 bits.

A DNA column has equal A,C,G,T frequencies. What is its information content?

0 bits.

True or false: More information content means a taller total logo stack.

True.

What is the maximum DNA sequence-logo information content?

2 bits.

What is the maximum protein sequence-logo information content?

log2(20) ≈ 4.32 bits.

Does observed sequence distance always equal the number of substitutions?

No. Multiple changes at one site can be hidden.

A changes to G and back to A. How many differences are observed at the end?

Zero, despite two substitutions.

True or false: p-distance can underestimate evolutionary distance.

True.

What does p-distance measure?

Fraction of compared positions that differ.

Why apply a correction such as Jukes-Cantor?

To estimate hidden substitutions beyond observed differences.

What does a phylogenetic branch length usually represent?

Amount of evolutionary change.

How do you find distance between two tips on a tree?

Sum branch lengths along their connecting path.

What is the first step of UPGMA?

Join the closest pair in the distance matrix.

UPGMA joins two tips separated by distance 8. What is each initial branch length?

4.

Which assumes a molecular clock: UPGMA or Fitch-Margoliash?

UPGMA.

True or false: UPGMA is reliable even when evolutionary rates vary greatly.

False. Its molecular-clock assumption may be violated.

Which method fits branch lengths to pairwise distances: UPGMA or FM?

Fitch-Margoliash.

Does FM require the same constant-rate assumption as UPGMA?

No.

Which method typically produces a rooted ultrametric tree?

UPGMA.

A and B are merged in UPGMA. How is distance to C updated?

Average the distances from members of cluster AB to C.

True or false: A small observed distance always proves a recent common ancestor.

False. Rates and repeated substitutions can complicate interpretation.

What information is lost when sequences are reduced to a distance matrix?

Site-by-site sequence patterns.

For a three-tip tree, what is distance A–B in terms of branches a and b?

a + b.

What does the Markov property say about the next state?

It depends only on the current state.

True or false: A first-order Markov chain needs the entire past to predict the next state.

False.