Lecture 3

Procedue of comparing two or more sequences by searching for a series of individual characteris that are in the same order in the sequence

Significance of Sequence Alignment

process of lining up two sequences to achieve maximal levels of identity and show conservation of residues

used to assess degree of similarity and possibly homology

term thats refers to the same residues between two proteins; may be in global or local alignment

term that referes to residues have structural or functional related; can only use “higher/lower degree of similarity”

sum of both identical and similar residues; goal of pairwise alignment

Calculating percent similarity, steps

Formula for percent similarity

Refers to the exact match between two nucleotide or amino acids

refers to a resemblance between two residues that is greater than one would expect at random

• Simple fraction of identical residues • genetic distances based on models of DNA sequence evolution

Genetic distances based on models of AMINO ACID sequence evolution - measured using matrices

Example of matrices used to measure peptide sequences

a sequences that share a common evolutionary ancestry

sequence regions that are homologous are also called _____

share a common evolutionary ancestry

derived from a single ancestral gene in the Least Common Ancestor

two or more homologous genes found within a single species • duplicated genes with the some genome, may evolve new function

Two types of pairwise comparison

Example of Graphical Analysis

Types of Residue/Residue analysis

• visually compares two sequences (like DNA, RNA, or protein) on a 2D grid, placing a dot for each matching character to highlight similarities and identify repeats, insertions, or deletions through graphical pattern

• Compares the sequences as a whole • analyzes polymorphism between closely related sequences