Multiple Sequence Alignments

What is the main purpose of a Multiple Sequence Alignment (MSA)?

To compare many sequences at once in order to identify conserved positions, functional region, domains and evolutionary relationship

Why are conserved residues important in MSA?

They are often evolutionarily preserved and indicate functional or structural importance

What biological questions can MSA help answer?

Structural alignment, conserved positions, domain detection and phylogenetic relationship

WHat do insertions and deletions in an MSA often indicate?

Surface loops or flexible regios in protein structure

What does a conserved glycine or proline often suggest?

A beta-turn in protein structure

What pattern of conserved hydrophobic residues suggests an alfa-helix?

Conserved residues at positions i, i+3, i+4, i+7, indicating one helix face packed into the protein core

Why are conserved cysteines significant?

Cysteine is rare and often forms disulfide bonds, important for protein stability

What is the Sum-of-Pairs (SP) score in MSA?

The total alignment score calculated by summing scores for all pairwise alignments within the MSA

Why is optimal MSA computation difficult?

The problem is computationally hard and scales exponentially with the number of sequences

What is progressive alignment?

A heuristic method that builds an MSA step-by-step by aligning the most similar sequences first, guided by a tree

What is a guide tree used for in progressive alignment?

To determine the order in which sequences or alignments are combined

What is a sequence logo?

A graphical representation of an MSA showing residue conservation at each position

What determines the height of letters in a sequence logo?

The frequency of each residue at that position

What does the total height of a sequence logo column represent?

The information content (measured in bits)

What is the maximun information content for nucleotides?

2 bits

What is the maximum information content for amino acids?

log₂(20) ≈ 4.3 bits

What is a Position-Specific Scoring Matrix (PSSM)?

A matrix derived from an MSA that scores residues differently at each position based on observed frequencies

How does a PSSM differ from BLOSUM62?

BLOSUM62 is position-independent, while PSSMs are position-specific

Why are pseudocounts used when building a PSSM?

To compensate for lack of fata and avoid zero probabilities

What is PSI-BLAST?

An iterative search method that builds a PSSM from initial hits and uses it to find more distant homologs

What is the main advantage of iterative sequence searches?

They detect more distant homologs than standard pairwise searches