Lecture 10 Assignments - BIO454

Lecture 10, BIO454 Student Assignments

• Lecture 10 of BIO454 course, focused on student assignments.

Outline

• Identity
• Score
• E-value and P-value
• Phylogenetic tree
• Threshold
• BLAST

Identity

• Sequence identity is the number of matching characters between two sequences.
• Example: If two sequences, each with 720 nucleotides, have 648 matching nucleotides, the identity is 90% (648/720).
• 100% identity means no gaps and all characters match.

Score

• A score is a numerical value indicating alignment quality.
• Higher scores indicate higher similarity.
• Score depends on the scoring system (substitution, gap).
• Substitution: Non-identical nucleotide/amino acid at a position in an alignment.
• Gap: Space introduced in an alignment to account for insertions/deletions in one sequence relative to another.
• Maximum score occurs when a sequence is compared to itself.

How to Calculate Score

• Score is the sum of substitution and gap scores.
• Substitution scores are from a look-up table (a table of values for nucleotide/amino acid substitutions).

How to Calculate Gap Scores

• Gap scores are the sum of gap open penalty (G) and gap extension penalty (L) penalties.
• Gap cost = G + Ln, where n is the gap length.
• High G (gap opening) and low L (gap extension) values are given for gaps. Example: (10-15) and (1-2).

Example Calculation of Score

• Example alignment scores are provided and calculated using substitution and gap scores.

E-Value

• E-value (expected value) estimates the number of sequences in a database that would be expected, by chance, to align equally or more significantly to the query than the found hit, based on a random search.
• Lower E-value indicates a better hit.
• E-value depends on the query's length and the database size.
• Example: E-value of 0.05 suggests a 5 in 100 chance of the alignment occurring by chance.
• A high E-value indicates many hits, possibly of low quality.

P-Value

• P-value is the probability of a chance alignment occurring with a particular score.
• Calculated by relating observed alignment score (S) to the expected distribution of scores from random sequences.
• Important to note that p-values are different from E-values, but both measure the significance of alignments.
• Very small p-values (closer to 0) point to a highly significant alignment, suggesting the alignment isn't by chance.

P-value and E-value Comparison

• E-value is a frequency metric, while p-value is a probability metric.
• E-value represents the number of better alignments expected, by chance, while the p-value represents the likelihood of the match occurring by chance.
• Statistically, the e-value is a correction for the p-value in multiple testing situations.

Threshold

• Threshold specifies the similarity percentage requirement for an alignment to be considered significant in DotMatcher comparisons between sequences.
• Example thresholds: 100%, 80%, 60%, 20%
• Each threshold requires a certain proportion of matching amino acids within a specific window/segment of the sequence to meet the defined threshold.

BLAST

• BLAST (Basic Local Alignment Search Tool) is an algorithm used for sequence comparison (e.g., amino-acid sequences of proteins, DNA/RNA sequences).
• BLAST uses a numerical score to represent alignment quality, with higher scores indicating better similarity.

Phylogenetic Tree

• A phylogenetic tree (dendrogram) visually represents evolutionary relationships among organisms.
• Based on similarities/differences in physical/genetic characteristics.
• Each node represents a common ancestor, with branches extending to descendant species.
• Similar species are more closely related, sharing a more recent ancestor. More distant species have less relatedness and less recent common ancestors.

Why Study Phylogenetic Trees?

• Understanding human origins
• Biogeography (dispersal vs. vicariance)
• Evolutionary tempo (e.g., Cambrian explosion)
• Origin of traits
• Molecular evolution processes
• Disease origins (e.g., AIDS)

Full Example of Calculating Phylogenetic Tree Distance

• Several tables are provided showing data for calculating phylogenetic tree distances, examples of new average distance calculation, and clustering trees.