Bioinformatics II: Alignment & Similarity

These flashcards cover the key terms and concepts from the 'Bioinformatics II: Alignment & Similarity' lecture notes.

Alignment

The arrangement of sequences to identify similarities and differences.

Similarity

The degree to which sequences share common characteristics.

BLAST

Basic Local Alignment Search Tool, a program that finds regions of local similarity between sequences.

Homologous sequences

Sequences that share a common ancestor.

Pairwise alignment

Comparison of two sequences to identify similarities and differences.

Multiple sequence alignment (MSA)

Comparison of three or more sequences simultaneously.

Dotplot

A graphical method for comparing two sequences by plotting similarities.

Gaps

Insertions or deletions in an alignment to improve match accuracy.

Global alignment

Aligns two sequences across their entire length.

Local alignment

Identifies regions of highest similarity between sequences.

Substitution matrix

A scoring system used to evaluate the similarity of aligned sequences.

PAM

Point Accepted Mutation, a scoring system for protein sequence alignment.

BLOSUM

Block Substitution Matrix, a scoring matrix for protein alignments.

E-value

The expected number of matches by chance in a BLAST search; lower values indicate more significant matches.

Scoring system

A method to assign values to an alignment to determine the best fit.

Mismatches

Positions in an alignment where the residues differ.

Indel

An insertion or deletion in the sequence alignment.

Conservation

The preservation of certain residues across different sequences.

Residue

An individual unit of a sequence, such as an amino acid or nucleotide.

Evolutionary conserved regions

Parts of sequences that are similar across different species due to common ancestry.

Sequence retrieval

The process of obtaining specific sequences from databases.

Gene products

Proteins that are translated from genes.

Development of algorithms

Creation of methods to efficiently compare sequences.

Biochemical similarity

The degree to which sequences share similar chemical properties.

Mutation frequencies

The rates at which genetic changes occur.

Query sequence

The sequence used as a baseline in a BLAST search.

Accession number

A unique identifier given to a nucleotide or protein sequence in a database.

Protein sequence

A sequence of amino acids in a protein.

Nucleotide sequence

A sequence of nucleotides in DNA or RNA.

Conserved regions

Segments of sequences that remain unchanged throughout evolution.

Gene annotation

The process of identifying and assigning functions to genes.

Dotplot matrix

A visual representation of similarity between two sequences in a dotplot format.

Alignment scoring

Evaluating alignments based on match, mismatch, and gap penalties.

Similarity search

Finding sequences in a database that resemble a given sequence.

Evolutionary biology

The study of how sequences evolve over time.

Interpreting BLAST results

Analyzing the output from a BLAST search to draw conclusions about sequence similarities.

Homology

The state of having the same or similar relation.

Function prediction

Using alignment data to infer the biological role of sequences.

Consensus sequence

A sequence that represents the most common residues at each position in aligned sequences.

Taxonomic groups

Categories for classifying organisms based on shared features.

Output format

The way data is presented after a scientific computation.