Computational Molecular Microbiology Quiz

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Questions and Answers

What are some examples of genes where adaptive selection is observed, according to the provided text?

Genes involved in pathogen defense/recognition interaction, genes in pathogens to overcome our immune systems, and vertebrate lysozymes (diet).

What are some tools/resources mentioned in the text for studying selection and sequence variation?

https://www.hiv.lanl.gov/content/sequence/SNAP/SNAP.html, https://www.hiv.lanl.gov/content/sequence/CodonAlign/codonalign.html, http://www.datamonkey.org/, http://www.datamonkey.org/busted, https://www.hiv.lanl.gov/content/sequence/HIV/links.html, http://www.ub.edu/dnasp/, https://tanguay.info/learntracker/page/lectureNotesItems.idCode=molecularclock, http://www.lecb.ncifcrf.gov/~toms/sequencelogo.html, http://weblogo.berkeley.edu/, http://weblogo.threeplusone.com/create.cgi

What is the molecular-clock hypothesis and how is it related to DNA sequences?

The molecular-clock hypothesis states that DNA sequences in a genome change through spontaneous mutation at a constant rate. It can be used to estimate how long ago two species diverged from a common ancestor.

What is the purpose of a sequence logo and what does it display?

A sequence logo displays the frequencies of bases or amino acids at each position in a sequence. It is used to show conservation for binding sites, promoter regions, etc. Signup and view all the answers

What is the alternative tool mentioned for finding conserved or visually displaying conserved regions in DNA or amino acid sequences?

Weblogo (<a href="http://weblogo.berkeley.edu/">http://weblogo.berkeley.edu/</a>) Signup and view all the answers

What type of alignment is needed for creating sequence logos?

Multiple alignment in either fasta or CLUSTAL W(X) format. Signup and view all the answers

What can the sequence logos be used to display?

Conservation for binding sites, promoter regions, etc. Signup and view all the answers

What is the purpose of the mentioned DNA polymorphisms tool (http://www.ub.edu/dnasp/)?

To analyze DNA polymorphisms. Signup and view all the answers

What is the Newick notation for the tree with leaf nodes A, B, C, and D?

(A,B,(C,D)) Signup and view all the answers

What is the New Hampshire tree format for the tree with leaf nodes 13Xerula, 4Gymnopus, 3Gymnopus, 11Marasmiu, 12Hemimyce, 9Hydropus, 10Megacoll, 5Clitocybu, 7Mycena, 8Mycena, Macrolepio, Melanophyl, Laccaria-l, 2Tephrocyb, 1Tephrocyb, 2Lyophyllu, 1Lyophyllu, Lepista-ir, Clitocybe-, Tricholoma, Hypsizygus, LH10, LH7, LH6, LH5, and LH2?

(13Xerula:0.20742,(4Gymnopus:0.01799,3Gymnopus:0.01655):0.18973, (11Marasmiu:0.13171,(((12Hemimyce:0.10126,(((9Hydropus:0.18929, 10Megacoll:0.16889):0.07927,5Clitocybu:0.10161):0.05273,(7Mycena:0.12563, 8Mycena:0.08566):0.06746):0.03878):0.06105,(((Macrolepio:0.07506, Melanophyl:0.07776):0.07589,Laccaria-l:0.06483):0.03329,(((2Tephrocyb:0.03985, (1Tephrocyb:0.02172,(2Lyophyllu:0.01327,1Lyophyllu:0.01128):0.01244):0.01147):0.03053, (Lepista-ir:0.04695,Clitocybe-:0.02680):0.01156):0.01228,(Tricholoma:0.02023, Hypsizygus:0.01816):0.01950):0.04363):0.03321):0.03312,((LH10:0.00000, LH7:0.00000):0.00276,(LH6:0.00000,LH5:0.00000,LH2:0.01095):0.00254):0.12640):0.08161):0.12332) Signup and view all the answers

What does the output from bootstrap analysis Sepboot-->DNApars provide in the treefile?

Leaf nodes and distances Signup and view all the answers

What type of analysis is used to generate the treefile output (bootstrap analysis: Sepboot-->DNApars)?

Bootstrap analysis Signup and view all the answers

What is the purpose of ancestral sequence reconstruction in phylogenetic analysis?

Ancestral sequence reconstruction aims to infer the sequences of ancestral genes or proteins at different nodes of a phylogenetic tree, providing insights into the evolutionary history of those sequences. Signup and view all the answers

How is the concept of selection (dN/dS) relevant in the context of alignment analysis?

The concept of selection (dN/dS) is used to assess the evolutionary forces acting on protein-coding genes, where dN represents the rate of non-synonymous substitutions and dS represents the rate of synonymous substitutions. This ratio provides information about the selective pressure on the gene. Signup and view all the answers

What is the significance of SYNSCAN analysis in identifying gene selection and functional constraints?

SYNSCAN analysis is valuable for estimating gene selection and identifying functional constraints and neutral evolution. It can indicate whether a gene is under purifying selection, gaining new functions, or experiencing neutral evolution based on the dN and dS values. Signup and view all the answers

How does the neutral theory of evolution impact rates of substitutions and codon bias?

The neutral theory of evolution suggests that most evolutionary changes at the molecular level are caused by random genetic drift of neutral mutants. This theory has implications on the rates of substitutions, as well as codon bias, which may be influenced by neutral evolution. Signup and view all the answers

What are the requirements outlined for using SYNSCAN or MEGAX for selection options?

The text outlines the importance of assembling alignments without indels when utilizing SYNSCAN or MEGAX for selection options. This requirement ensures accurate estimation of gene selection and functional constraints. Signup and view all the answers

How does the concept of outgroup relate to rooting trees in phylogenetic analysis?

In phylogenetic analysis, an outgroup is a species or group of species that is closely related to the ingroup (the group of primary interest) but is not part of it. Outgroups are useful for rooting trees, providing a reference point for the direction of evolutionary change. Signup and view all the answers

What is the role of the FASTML Server in ancestral sequence reconstruction?

The FASTML Server is used for computing Maximum Likelihood ancestral sequence reconstruction, providing a computational tool for inferring ancestral sequences and understanding evolutionary relationships among sequences. Signup and view all the answers

How can sequence logos be utilized in the context of alignment analysis?

Sequence logos are graphical representations of the patterns within a multiple sequence alignment. They can be used to visualize conserved regions, sequence variability, and potential functional motifs within protein-coding genes. Signup and view all the answers

What are the potential limitations of using dN and dS values for entire genes in determining functionality?

Small changes in specific parts of a gene may lead to higher dN values, potentially affecting the overall interpretation of gene functionality. Therefore, using dN and dS values for entire genes may overlook localized changes that influence functionality. Signup and view all the answers

What program is discussed for estimating gene selection in the text, and what are its applications?

The text mentions SYNSCAN analysis as a program for estimating gene selection. Its applications include identifying genes under purifying selection, gaining new functions, and assessing the variability in dN and dS values. Signup and view all the answers

What online tool is mentioned for tree display in the text, and what is its name?

The text mentions iTOL as an online tool for tree display. iTOL stands for Interactive Tree of Life and provides a platform for visualizing phylogenetic trees with various customization options. Signup and view all the answers

How is the concept of rooting trees related to the use of the TreeView program?

The TreeView program is utilized for visualizing and manipulating phylogenetic trees. In the context of rooting trees, TreeView can be used to display rooted trees and explore the evolutionary relationships among different taxa. Signup and view all the answers

Study Notes

Phylogenetic Tree Analysis and Ancestral Sequence Reconstruction

The text contains a Newick notation representation of a phylogenetic tree involving various species of small mushrooms.
Bootstrap support values are provided for leaf nodes in the phylogenetic tree.
The text mentions an online tool for tree display called iTOL, and provides a link to it.
It discusses the use of the TreeView program and rooting trees, as well as the concept of outgroup in phylogenetic analysis.
Ancestral sequence reconstruction is described, and the FASTML Server for computing Maximum Likelihood ancestral sequence reconstruction is mentioned.
The text explains the concept of selection (dN/dS) and sequence logos in the context of alignment analysis.
SYNSCAN analysis, a program for estimating gene selection, is discussed, along with its application in identifying functional constraints and neutral evolution.
The neutral theory of evolution and its implications on rates of substitutions and codon bias are explained.
The text outlines the requirements for using SYNSCAN or MEGAX for selection options and emphasizes the importance of assembling alignments without indels.
It provides an example showing how SYNSCAN can indicate functional constraints or non-functionality in a gene of interest based on the dN and dS values.
The program's usefulness in identifying genes under purifying selection or gaining new functions is highlighted, along with the variability in dN and dS values.
The text discusses the potential limitations of using dN and dS values for entire genes in determining functionality, as small changes in specific parts of a gene may lead to higher dN values.

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Description

Test your knowledge of computational molecular microbiology with this quiz covering sequence databases, sequence comparison, pairwise alignment, multiple sequence alignment, phylogenetic tree building, and Newick notation. Brush up on your skills and challenge yourself with this quiz!