4 Sequence Alignment Free Online FlashCards

What does a sequence alignment represent?

It arranges DNA, RNA, or protein sequences so likely corresponding positions share columns. The alignment is a model of positional correspondence, not proof of shared evolutionary history.

When is a global alignment useful?

A global alignment spans both sequences end to end. It is useful when they are similar in length and expected to correspond across their full lengths.

What does a local alignment identify?

A local alignment finds the best-matching subsections and leaves unrelated flanking regions unaligned. It can reveal a shared domain or motif within longer sequences.

Which classic methods optimize global and local alignments?

Needleman–Wunsch finds an optimal global alignment under a chosen scoring scheme; Smith–Waterman finds an optimal local alignment.

What can a gap suggest, and what can it not establish?

A gap represents a proposed insertion or deletion relative to another sequence. Its presence alone does not establish where or when the evolutionary event occurred.

Why use substitution matrices in protein alignment?

Protein alignments use substitution matrices such as BLOSUM or PAM to score replacements. BLOSUM matrices are derived from conserved protein sequence blocks.

What is the affine gap-cost formula?

An affine gap cost is $\text{gap cost}(k)=-(a+bk)$, where $a$ is the opening penalty and $b$ is the per-residue extension penalty.

What effect does an affine gap penalty tend to have?

Affine gap costs penalize opening a gap more than extending it. This tends to favor one longer gap over several separate short gaps.

What does a BLAST E-value estimate?

A BLAST E-value estimates how many alignments with a score at least that good would be expected by chance in a search of that size. Lower values generally indicate stronger evidence against a chance match.

What is a multiple sequence alignment?

A multiple sequence alignment aligns three or more sequences in shared columns, helping reveal patterns such as conserved motifs or variable positions.

How do progressive MSA methods generally build an alignment?

Progressive methods estimate similarities, build a guide tree, align closer sequences or groups first, then add more distant ones. Early errors can affect later steps.

What does a sum-of-pairs score calculate?

A sum-of-pairs score adds scores for residue pairs across alignment columns. It is one way to evaluate a multiple sequence alignment.