Computational Molecular Microbiology (MBIO 4700) Quiz

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Questions and Answers

Which notation is commonly used to represent phylogenetic trees?

Edinburgh notation

Newick notation (correct)

Manchester notation

Hampshire notation

What type of analysis can produce a treefile as an output?

Bootstrap analysis (correct)

Sequence alignment

Pairwise alignment

Phylogenetic comparison

Which software is commonly used for visualizing phylogenetic trees?

BranchGraph

TreeViz

FigTree (correct)

PhyloDraw

What does the Newick notation (((A:0.1,B:0.2):0.3,C:0.4):0.5) represent?

A phylogenetic tree with branch lengths Signup and view all the answers

What is the main focus of the HIV Signature and Sequence Variation Analysis by Korber B. (2000)?

Analyzing HIV molecular sequences Signup and view all the answers

What is the purpose of a sequence logo?

Displaying frequencies of bases/amino acids at each position Signup and view all the answers

What is the function of the tool Weblogo?

Creating sequence logos Signup and view all the answers

What is the purpose of the tool SNAP (Synonymous Non-synonymous Analysis Program)?

Analyzing synonymous and non-synonymous mutations in genes Signup and view all the answers

What does the molecular-clock hypothesis propose?

$DNA$ sequences change through spontaneous mutation at a constant rate Signup and view all the answers

What do sequence logos visually display?

Frequencies of bases/amino acids at each position in a sequence Signup and view all the answers

What is the main focus of the tool BUSTED (Branch-site Unrestricted Statistical Test for Episodic Diversification)?

Detecting episodic diversifying selection in genes Signup and view all the answers

What is the purpose of the tool CodonAlign?

Aligning codon sequences for analysis Signup and view all the answers

What is the FASTML Server used for in the context of ancestral sequence reconstruction?

Inferring Maximum Likelihood ancestral sequences Signup and view all the answers

Which program is described as being useful for estimating if a gene is under selection or drifting?

SYNSCAN analysis Signup and view all the answers

What type of selection or constraint does dS > dN indicate?

Purifying selection or functional constraint Signup and view all the answers

In the context of dN/dS ratios, what does dN = dS indicate?

Nonfunctional genes Signup and view all the answers

What does the neutral theory of evolution primarily analyze?

Rates of substitutions and codon bias Signup and view all the answers

What are the requirements for conducting SYNSCAN or MEGAX analysis?

Codon-based alignment in fasta format Signup and view all the answers

What is emphasized when examining evidence of change due to chance or selection?

Sequence logos Signup and view all the answers

Which tool is NOT mentioned for visualizing and interacting with phylogenetic trees?

MEGAX Signup and view all the answers

What does the variability of dN/dS ratios indicate?

Sometimes only a small part of the protein changes to gain a new function, leading to variable ratios. Signup and view all the answers

What does the concept of SYNSCAN analysis focus on determining?

Functional constraints on genes Signup and view all the answers

Study Notes

Phylogenetic Tree Analysis and Ancestral Sequence Reconstruction

The provided data includes a phylogenetic tree of small mushroom species, with bootstrap support values at the leaf nodes.
A Newick notation is used to represent the phylogenetic relationships between the species.
The text discusses the use of various tools for visualizing and interacting with phylogenetic trees, such as iTOL, TreeView, FigTree, and others.
Ancestral sequence reconstruction is mentioned, with references to the FASTML Server for computing Maximum Likelihood ancestral sequences.
The concept of selection (dN/dS) and sequence logos is explained, with an emphasis on examining evidence of change due to chance or selection.
SYNSCAN analysis, a program for estimating if a gene is under selection or drifting, is described with its application in determining functional constraints.
The text discusses the neutral theory of evolution and its application in analyzing rates of substitutions and codon bias.
The requirements for conducting SYNSCAN or MEGAX analysis are outlined, including the need for a codon-based alignment in fasta format.
The text explains the implications of specific dN/dS ratios, with dS > dN indicating purifying selection or functional constraint.
The program is useful for identifying nonfunctional genes (dN = dS) or those gaining new functions (dN > dS).
It is highlighted that dN values for entire genes might only be slightly higher than dS, as changes to gain new functions may occur in only a small part of the protein.
The variability of dN/dS ratios is noted, as sometimes only a small part of the protein changes to gain a new function, leading to variable ratios.

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Description

Test your knowledge on computational molecular microbiology topics including sequence databases, sequence comparison, pairwise alignment, multiple sequence alignment, phylogenetic tree, and Newick notation.