Bioinformatics: BLAST, Multiple Sequence Alignment, and Phylogenetics

Vocabulary flashcards based on lecture notes covering BLAST tools, Multiple Sequence Alignment (MSA) methodologies, and phylogenetic tree construction principles.

BLAST

Basic Local Alignment Search Tool used to identify similar DNA or protein sequences.

Query Sequence

The sequence submitted for comparison in a BLAST search.

Subject Sequence

The matching sequence found in the database during a BLAST search.

Heuristic Algorithm

A fast search strategy that finds good matches without testing every possibility, used by BLAST.

HSP (High-Scoring Segment Pair)

A region of strong local similarity between two sequences.

E-value

The expected number of matches with a similar score that could occur by chance; lower values indicate more significant matches.

Bit Score

A normalized numerical score representing alignment quality that allows comparison between BLAST searches.

Query Coverage

The percentage of the query sequence included in the alignment.

Identity

The exact percentage of matching residues between sequences.

Similarity

The degree of resemblance between sequences, including both exact matches and conservative substitutions.

Homology

Similarity due to shared evolutionary ancestry; it is not expressed as a percentage.

BLASTn

A BLAST search comparing DNA against a DNA database.

BLASTP

A BLAST search comparing protein against a protein database.

BLASTX

A BLAST search comparing translated DNA against a protein database.

PSI-BLAST

Iterative BLAST that builds a profile to detect distant homologues.

Smith-Waterman

An algorithm that guarantees the optimal local alignment but is much slower than BLAST.

Multiple Sequence Alignment (MSA)

The alignment of three or more DNA or protein sequences to identify conserved regions and infer evolutionary relationships.

Conserved Region

A sequence region that remains similar across multiple organisms.

Consensus Sequence

A summary sequence showing the most common residue at each position in an alignment.

Clustal Omega

A fast, progressive multiple sequence alignment program.

MUSCLE

A high-accuracy multiple sequence alignment program that uses iterative refinement.

Phylogenetics

The study of evolutionary relationships among organisms or genes.

Phylogenetic Tree

A branching diagram showing inferred evolutionary relationships.

Orthologs

Homologous genes separated by speciation that usually retain similar functions.

Paralogs

Homologous genes produced by gene duplication that may evolve new functions.

Molecular Clock

A method for estimating evolutionary time based on the idea that mutations accumulate at an approximately constant rate.

Bootstrap Value

A measure of confidence for branches in a phylogenetic tree.

UPGMA

A distance-based tree-building method that assumes a constant evolutionary rate.

Neighbour Joining

A distance-based tree-building method that does not assume a molecular clock.

Maximum Parsimony

A method that chooses the phylogenetic tree requiring the fewest evolutionary changes.

Maximum Likelihood

A method that chooses the tree with the highest probability under a specific evolutionary model.

Rooted Tree

A phylogenetic tree that shows the common ancestor of all sequences.

Unrooted Tree

A phylogenetic tree that shows relationships between sequences only, without identifying a common ancestor.