22 Questions
Which notation is commonly used to represent phylogenetic trees?
Newick notation
What type of analysis can produce a treefile as an output?
Bootstrap analysis
Which software is commonly used for visualizing phylogenetic trees?
FigTree
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
What is the main focus of the HIV Signature and Sequence Variation Analysis by Korber B. (2000)?
Analyzing HIV molecular sequences
What is the purpose of a sequence logo?
Displaying frequencies of bases/amino acids at each position
What is the function of the tool Weblogo?
Creating sequence logos
What is the purpose of the tool SNAP (Synonymous Non-synonymous Analysis Program)?
Analyzing synonymous and non-synonymous mutations in genes
What does the molecular-clock hypothesis propose?
$DNA$ sequences change through spontaneous mutation at a constant rate
What do sequence logos visually display?
Frequencies of bases/amino acids at each position in a sequence
What is the main focus of the tool BUSTED (Branch-site Unrestricted Statistical Test for Episodic Diversification)?
Detecting episodic diversifying selection in genes
What is the purpose of the tool CodonAlign?
Aligning codon sequences for analysis
What is the FASTML Server used for in the context of ancestral sequence reconstruction?
Inferring Maximum Likelihood ancestral sequences
Which program is described as being useful for estimating if a gene is under selection or drifting?
SYNSCAN analysis
What type of selection or constraint does dS > dN indicate?
Purifying selection or functional constraint
In the context of dN/dS ratios, what does dN = dS indicate?
Nonfunctional genes
What does the neutral theory of evolution primarily analyze?
Rates of substitutions and codon bias
What are the requirements for conducting SYNSCAN or MEGAX analysis?
Codon-based alignment in fasta format
What is emphasized when examining evidence of change due to chance or selection?
Sequence logos
Which tool is NOT mentioned for visualizing and interacting with phylogenetic trees?
MEGAX
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.
What does the concept of SYNSCAN analysis focus on determining?
Functional constraints on genes
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.
Test your knowledge on computational molecular microbiology topics including sequence databases, sequence comparison, pairwise alignment, multiple sequence alignment, phylogenetic tree, and Newick notation.
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