Lecture 10 Assignments

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Questions and Answers

What does a lower p-value indicate in terms of significance?

It shows that the alignment is less significant.

It suggests the alignment occurred by chance.

It indicates a higher similarity between sequences. (correct)

It relates to the expected alignment score.

How does the E-value differ from the p-value?

P-value is a probability metric. (correct)

P-value indicates a frequency metric.

E-value is calculated based on random sequence comparisons.

E-value represents the score quality of an alignment.

What is the purpose of a phylogenetic tree?

To compare the nucleotide sequences of organisms.

To display the protein sequence alignments.

To represent evolutionary relationships among species. (correct)

To analyze scoring systems used in BLAST.

How is identity defined in the context of sequence comparison?

The percentage of similar characters between two different sequences. Signup and view all the answers

What does a higher BLAST score indicate?

Better alignment and higher similarity. Signup and view all the answers

What is the implication when the identity between two sequences is 100%?

The sequences are identical with no differences. Signup and view all the answers

Which statement correctly describes how to calculate the score of an alignment?

The score is the sum of substitution scores and gap scores. Signup and view all the answers

What does the threshold percentage determine in the DotMatcher?

The extent of similarity required for plotting. Signup and view all the answers

What does a lower E-value signify in sequence alignment?

The alignment is less likely to occur by chance. Signup and view all the answers

Which statement is true regarding the common ancestor in a phylogenetic tree?

Species with recent common ancestors are more closely related. Signup and view all the answers

What factors influence the E-value of a sequence alignment?

The query sequence length and the size of the database. Signup and view all the answers

Which aspect is covered by understanding phylogenetic trees?

Origin and dispersal patterns of diseases. Signup and view all the answers

What is the function of gap penalties in scoring an alignment?

To account for insertions and deletions between sequences. Signup and view all the answers

What type of data does BLAST compare?

Genetic sequences of proteins and nucleotides. Signup and view all the answers

What does it mean when the E-value is reported as 0.05?

There is a 5% chance of the alignment occurring randomly. Signup and view all the answers

What is represented by the maximum score in sequence comparison?

The alignment score when comparing a sequence with itself. Signup and view all the answers

Signup and view all the answers

Study Notes

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.

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Description

This quiz explores key concepts from Lecture 10 of the BIO454 course, specifically focusing on student assignments. Topics include sequence identity, scoring systems for alignment, and the use of E-values and P-values in bioinformatics. Test your understanding of phylogenetic trees and the BLAST algorithm.

Lecture 10 Assignments - BIO454

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