bioinformatics quiz 3

pairwise alignment

models homology between two sequences

Multiple Sequence Alignment

simultaneously aligns three or more sequences by inserting gaps to maximize overall similarity

Markov Model

substitution model assumes that nucleotide or amino acid changes depend only on the currently observed state and not on previous history, effectively making the chain "without memory"

Percent Accepted Mutation (PAM) substitution matrix

Based on global alignments of closely related proteins; it is best for evolutionary and phylogenetic studies

BLOSUM (Blocks Substitution Matrix)

Based on local alignments; it is the default for database searches like BLAST

Gaps and Indels

Gaps represent insertions or deletions (indels) in an evolutionary context. In the affine gap penalty model, it is more "expensive" to open a new gap than to extend an existing one.

The Clustal Method

This is a progressive profile alignment method that uses a guide tree to determine the order in which sequences are joined to the alignment.

phylogeny

a model of relationships between biological entities (organisms, genes, or proteins) based on common ancestry

External Nodes (Leaves/Tips)

Represent the actual taxa, OTUs, or sequences being compared.

Internal Nodes

Represent hypothetical ancestors where lineages diverged.

The Root

A special internal node representing the common ancestor of all taxa in the tree.

Branches (Edges)

Represent relationships; in phylograms (dendrograms), branch lengths are proportional to evolutionary distance or time, whereas in cladograms, they are not

Tree Rotation

Relationships between organisms do not change if a clade is rotated 180 degrees around an internal node

Rooting and the Outgroup

An unrooted tree shows relationships but not the evolutionary path. To root a tree, an outgroup—a taxon known to be unrelated to the others—is used to provide a starting point.

Homology

This refers to sequences or structures that share a common ancestor; sequences can only be compared meaningfully if they are homologous.

Orthologs

Homologs that diverged due to a speciation event

Paralogs

Homologs that diverged due to gene duplication.

Monophyletic (Clade)

Includes a common ancestor and all of its descendants.

Paraphyletic

Includes a common ancestor but only some descendants

Polyphyletic

A group whose members have different ancestors

Neighbor Joining (NJ)

An algorithmic method that is fast and based on a distance matrix; it produces a single draft phylogeny

Maximum Parsimony (MP)

An optimality criterion method that chooses the tree requiring the smallest number of evolutionary changes

Maximum Likelihood (ML)

A probabilistic method that uses substitution models to find the tree with the highest probability of producing the observed data

Bayesian Inference

Recommended for complex trees, it uses Markov Chain Monte Carlo (MCMC) simulations to determine the posterior probability of branches

Bootstrap Analysis

A permutation test that repeatedly re-samples the alignment data to see how often a specific branch appears in the resulting trees, indicating the robustness of that branch

16S rRNA Gene

The "gold standard" for prokaryotic classification because it is universal in all prokaryotes and forms the backbone of ribosomes, making it both conserved within species and variable between “species.”

SNP (Single Nucleotide Polymorphism)

A mutation involving a change in a single nucleotide at a specific position.

Heuristic Tree Search

A strategy used when comparing every possible tree is computationally impossible; it only searches for trees with the highest probability

P-distance

Calculated by dividing the number of nucleotide differences by the total number of sites