This lesson introduces multiple sequence alignment (MSA), how an alignment is represented, and why researchers compare several biological sequences at once.
A multiple sequence alignment is an arrangement of three or more biological sequences—usually protein, DNA, or RNA—so that corresponding positions can be compared in columns. An alignment is constructed by inserting gaps into the original sequences where needed. A gap is a placeholder, commonly shown as a hyphen, that represents a possible insertion or deletion during evolutionary history.
All flashcards
What is a multiple sequence alignment?
An arrangement of three or more biological sequences in equal-length rows, using inserted gaps to make corresponding positions comparable.
What does a gap represent in an alignment?
A placeholder used to align sequences; it may reflect an insertion or deletion in evolutionary history, but the alignment alone does not establish which event occurred.
What is a conserved position?
An alignment column in which the same or similar residues occur across multiple sequences. Conservation can suggest functional or structural importance.
What are indels?
Insertions and deletions—evolutionary events that add or remove residues relative to another sequence.
How can an aligned sequence be returned to its original form?
Remove its gap characters. The remaining residues should retain their original order.
Quiz questions
In progressive alignment, how does a guide tree usually order sequence additions?Answer: More similar sequences are aligned before more distant ones.
What does a hidden Markov model (HMM) use to represent alignment possibilities?Answer: Probabilities assigned to possible matches, mismatches, and gaps.
What distinguishes iterative alignment methods from strictly progressive methods?Answer: They can revisit earlier alignment decisions by realigning sequences or subsets.
In sequence analysis, what does homology mean?Answer: An evolutionary relationship through common ancestry.
What limitation is shared by heuristic MSA methods?Answer: They can find useful alignments without guaranteeing a global optimum.