Computational Molecular Microbiology Quiz

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

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

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.

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.

Weblogo (http://weblogo.berkeley.edu/)

Multiple alignment in either fasta or CLUSTAL W(X) format.

Conservation for binding sites, promoter regions, etc.

To analyze DNA polymorphisms.

(A,B,(C,D))

(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)

Leaf nodes and distances

Bootstrap 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.