Class 1
Goals:
- Know how to contact the instructor and TA.
- Know how your performance will be assessed and graded.
- Know that take-home exams and computer lab assignments are an important part of this course, and that they will be graded.
- Understand the concept of homology (continued in class 2)
- Understand the significant similarity between two primary protein sequences (that are not of low complexity) is a strong indication that the two sequences evolved from the same ancestral sequence.
Links:
Assignments for Wednesday (8/28):
- Read through the slides on homology
- Try to answer the following questions:
Would in your opinion maintaining a database on beetles that contains data on where was the beetle collected, its morphology, and where is it stored in the collection fall under bioinformatics?
Would in your opinion determining the 3D structure of a protein using X-ray crystallography fall under bioinformatics?
How many different proteins with length of 100 aa are theoretically possible?
At most how many aa substitutions does one need to turn one of these sequence into an another one?
- Formulate a question that you could ask on Wednesday (things
you didn't understand, anything you want to hear more details about).
Assignments for Friday (8/30):
- Read through the slides on protein structure
- Read following entries in Wikipedia:
- Fold an origami crane, write your name on the wings. We will use it as a flag in the class on Friday.
- If you want to keep personal copies of the things you do during the computer exercises, bring a laptop and/or memory stick to class on Friday.
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Class 2:
Goals:
- Rough outlines of replication. transcription and translation
- Understand the concepts of homology and convergent evolution as applied to biopolymers
- Understand why significant sequence similarity implies likely shared ancestry and similar function, but that the reverse (non-significant sequence similarity implies independent origin) is not true.
- Appreciate that the combinatoric space of all possible protein sequences is gigantic, but highly connected.
Links:
Assignments for Friday (8/30):
- Read through the slides on protein structure
- Read following entries in Wikipedia:
- Fold an origami crane, write your name on the wings. We will use it as a flag in the class on Friday.
- If you want to keep personal copies of the things you do during the computer exercises, bring a laptop and/or memory stick to class on Friday.
Assignment for Wednesday after Labor-day (9/4)
- Contemplate the following questions (see the slides on homology for inspiration):
Are most proteins with similar function homologous?
Are all proteins with similar function homologous?
Are most proteins with
significant sequence similarity homologous?
Do most homologous proteins have
significant sequence similarity?
Do most homologous proteins have
similar structure?
- Read the excerpt from Thomas Mann's book on Dr. Faustus (Dr Faustus) available on HuskyCT.
- How many different proteins with length of 100 aa are theoretically possible?
- At most how many aa substitutions does one need to turn one of these sequence into an another one?
- Formulate a question that you could ask on Wednesday (things
you didn't understand, anything you want to hear more details about).
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Goals Comp Lab 1:
- Launch chimera
- Display a 3 D coordinate file from the pdb (1HEW) in chimera
- Use different display settings
- Display amino acid side chains in the binding pocket of 1HEW and study the interactions between the substrate and the binding pocket.
- Calculate a Ramachandran plot, and determine where in this plot alpha helices, beta sheets, and glycine residues fall.
- Save your work as image and project.
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Class 3:
Goals:
- Understand the conceptual and empirical relationships between homology and sequence similarity;
- The role of gene duplication and sequence divergence in the evolution of proteins;
- Different ways new proteins emerge (duplication, domain shuffling, recruitment of non-coding sequences);
- Understand that RNA can be both genetic material and catalyst
- Know what else supports the RNA-world concept
- Item that support the RNA world concept, and difficulties faced by the RNA world
- The ATPsynthase as rotary motor (Yoshida's experiment, proteolipids)
Links:
Assignments for Friday (9/6):
Assignments for Monday (9/9):
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Goals Comp Lab 2:
- Have at least a rough understanding of the content of a protein data bank file
- Save individual subunits into distinct pdb files
- Align structures of divergent proteins
- Use the structure based alignment to align the linear sequences
- Align structures of a catalytic subunit during the catalytic cycle
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Class 4:
Goals:
- Know how RNA can be linked to the encoded protein in vitro
- Understand the principle behind the SELEX approach to evolve aptamers
- Know about the ATP binding peptide evolved from a random sequence and have an idea how this in vitro selection was accomplished
- Understand the implications this has for understanding convergent evolution
- Know under which conditions natural selection does occur.
- Know about the three domains of life (archaea, bacteria, eukaryotes) and how they are related to one another
- Appreciate that molecular evolution can study events that occurred before the last universal common ancestor
- Understand the role of ancient gene duplications in rooting the tree of life.
Links:
Slides on ATP binding sites as example for the power (or lack of power) of convergent evolution
Slides on ancient paralogs (we will revisit phylogenetic questions later in the semester in more detail)
Info on the Gaia hypothesis: http://en.wikipedia.org/wiki/Gaia_hypothesis
Info on the Medea hypothesis: https://en.wikipedia.org/wiki/Medea_hypothesis, https://www.ted.com/talks/peter_ward_on_mass_extinctions
Assignments for Wednesday 9/11
- Read through take-home exam #1 (posted on huskyCT)- Due on Friday
- Review the box below on Evolution through Natural Selection.
- Draw a sketch for the relation between the number substitutions that occurred in evolution and the the percent identity of the two sequences. (I.e. how does the observed similarity change, as more and more substitutions occur?)
What is the endpoint for 4 letter alphabet - for 20 letter alphabet.
- How does this relationship change, if some parts of the sequence are so important that the protein becomes non-functional, if a mutation occurs in these positions (i.e., these parts of the sequence are never observed to undergo any change?
- If substitution were to occur at a rate of 10^-8 per year and per site, how long would it take for two sequences to by less than 50% identical? (do a rough estimate ignoring multiple substitutions and back mutations.)
- If you were to do a realistic calculation and you were to consider a nucleotide sequence, how long would it take to arrive at 20% identity? (tip: how similar are to random sequences that have not been aligned?)
(Note: answering this should not require the use of a calculator or a formula, just common sense.)
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Class 5:
Goals:
- Understand the relation between substitutions and sequence divergence
- Know a few reasons why protein sequences work better to assess similarity than nucleotides
- What are inteins, and which enzymatic activities do they have?
- What are the possible symbiotic relationships between organisms, genes, or protein domains?
- What else contributes to evolution in addition to natural selection.
Links:
slides on inteins
class page (Box on evolution, Gaia, Jukes-Cantor)
Assignments for Monday 9/16
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Goals Comp Lab 3:
- Know how to
identify domains in multi domain proteins in chimera;
- inspect protein DNA interactions;
- identify the major and minor groove in a DNA molecule;
- create a multiple sequence alignment based on aligned structures in chimera
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Class 6:
Goals:
- Know about the tree and coral metaphors to depict evolution
- Appreciate Lamarck's contribution to understanding evolution.
- Understand the power and the limitations of the tree of life image.
- Understand the contributions that Woese and Fox made to the classification of life, which molecule they used, and the domains they discovered
- Understand the relationship between the 3 domains, and how the tree of life was rooted.
Links:
Slides on the Coral of Life - the tangled tree, gene transfer, exchange groups
Assignments for Wednesday 9/18
- Watch video on Snowball Earth (here)
- Watch video on reconstructing the Tree of Life
- What does the term phylogeny mean?
- TREE of LIFE overview here, (optional: compare here, here, here and here (especially the discussion is interesting).
- Read through Olga's Time-line of the Universe here
- Read through box in class 6 on "How old is life on Earth?"
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Class 7:
Goals:
- Know about metaphors for life's history, and why they were thought to be relevant (rhizome -, potato -, tree -, coral -, watershed of life)
- Appreciate that biology can provide negative feedback that tends to keep Earth's surface temperature constant (Gaia, Daisy world).
- Appreciate that biology can also trigger positve feedback loops (destruction of methane) that can move Earth's climate to an oscillation between CO2 greenhouse and snowball Earth.
- Appreciate Alan Turing's many contributions to science and society.
- Know about the discussion on competition and cooperation, social Darwinism and mutual aid.
- Understand that Darwin, while an abolitionist, was a child of this times.
- Know at least some processes in evolution that go beyond gradual evolution by natural selection
Links:
Slides on Mutual Aid, Natural selection, and metaphors to describe Life's history.
class page, Olga's time-line
Assignments for Friday 9/20
- Read through the file on frequently used formats here
- Explore the Genbank Sample file here
-
Assignments for Monday
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Goals Comp Lab 4:
- Know about bibliography software
- Know about the advantage of the databanks accessible through NCBI's Entrez.
- Be able to perform literature databank searches at Google scholar, Scopus and pubmed
- Know how to retrieve full length manuscripts
- Appreciate number usefulness of # of publications, # of citations, and the H-index
- Know how to access manuscripts similar to one that you know is relevant to you.
- Appreciate that GenBank is highly redundant
- Know that searches at the protein level are more effective than searches at the nucleotide level.
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Class 8
Goals:
- How to measure if sequences are significantly similar.
- Understand the difference between P and E values.
- Know about "usual" cut-offs for Z-scores, P- and E-values.
- Be able to discuss the process that may lead to the decay of significance
- Know what fishing expeditions are about
- Understand the BLAST is perfoming local alignments only
- Know what the Bonferoni correction is, and why it is not popular.
- Know what false positives and false negatives are in relation to a BLAST search
Links:
Webpage class 8
Def. of Bonferroni correction here; information on data dredging here
Assignments for Wednesday 9/25
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Class 9
Goals:
- Understand the problems that result from ownership of database entries.
- Appreciate the difference between supervised databanks and simple repositories.
- Appreciate the meaning and relationship between of E and P values
- Understand the BLAST is perfoming local alignments only
- Know what false positives and false negatives are in relation to a BLAST search
Links:
See the slides on blast searches
Assignment for Friday's class:
Assignments for Monday 9/30:
- Read through file on frequently used formats here
- Read the general Wikipedia entry on substitution matrices and on PAM and Blosum matrices - which one would you use for closely related, which ones for divergent sequences (here)?
- Read through the powerpoint slides from using BLAST to teach E-value-tionary concepts.
- Optional: Dan Graur wrote an introduction to his textbook "Intro to Molecular and Genome Evolution" (here) in which he argues that all of evolution boils down to changing allele frequencies. At least after a first reading this appears to embrace the modern synthesis, and does not consider symbiosis, holobionts and hologenomes (maybe one could argue that picking up a symbiont with new properties is equal to a mutation?). If you submit by next Wednesday a 1-2 page* (12pt font, line spacing 1.5, 1 inch margins) essay discussing/critiquing Dan Graur's introduction, it will be graded and may take the place of one of the takehome exams.
* Bibliography and figures to not count towards the page limit.
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Goals Comp Lab 5:
- Learn how to log into the xanadu cluster
- Use simple unix commands (cd, pwd, cat, more)
- learn how to redirect the output of a unix command to a file
- Perform pairwise sequence comparisons with PRSS and blast
- Databank searches with FASTA and blast.
- Appreciate the advantage of uniprot90 and uniprot50 for some questions you might try to answer through a databank search.
- Be aware the homology does not always extend to the complete protein sequence
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Class 10
Goals:
- Know which substitution matrices to use for comparing similar and for divergent sequences
- Understand the different types of error with as applied to data bank searches
- Know how to adjust significant levels of individual experiments to avoid fishing expeditions.
- Know who Margaret Dayhoff was and what contributions she made to modern molecular evolution and bioinformatics
- Know about PAM001, what it means and how is ti srelated to PAM200.
- Be able to discuss the advantages of the command-line in general and blast searches via the command-line in particular.
Links:
ppts slides that accompany "Using BLAST to Teach “E-value-tionary” Concepts"
See the slides on the history of genbank, PAM and Dayhoff
Slides on DNA sequencing
Assignments for Wednesday 10/2:
Assignment for Friday 10/4:
- Takehome exam #3 is due at 10.10am
- Think about how you will transfer files back and forth from the xanadu cluster.
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Class 11
Goals:
- Understand genome structure of prokaryotic genomes (Ori, leading/lagging strand, terminus of replication).
- Know two explanations that can explain the preponderance of recombination events between points equidistant to the origin of replication
- (co-occurrence of recombination with replication;
- AIMS and strand bias are not disrupted (i.e., these are the only recombination events that do not lead to a drop in fitness))
- Appreciate that Y-chromosome Adam and Mitochondrial Eve were not the only contributors to the gene pool of modern human
- Understand that the about 20,000 compatriots of mitochondrial Eve contributed their genetic information to today's human (but because of recombination these cannot be traced back in the genealogy).
- Know that the same is true for tracing genes in the tree of life (different genes trace to different ancestors).
- Understand the arguments for the domain ancestors being survivors of a catastrophe (impact?) that selected to thermophyly
Links:
Slides on strandbias and within genome recombination
Assignment for Monday 10/7
Study the Slides on strandbias and within genome recombination
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Goals Comp Lab 6:
- Understand how to run a blast search from the command-line.
- Be able to create a searchable database from a multiple fasta sequence file
- Know about different output formats, and be able to import blast search results into an Excel spreadsheet.
- Understand that %identity is not a good choice to assess significant sequence similarity.
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Class 12
Goals:
- Understand that %identity is not a good choice to assess significant sequence similarity.
- Understand the terminology used in cladistics
- Understand the concerns about not considering paraphyletic groups as proper taxonomic units
- Understand the multiple roots of the modern human populations
Links:
Assignment for Wednesday 10/9
- Think about questions for review session next Monday
- Read through take home assignment number 4 (posted later today. This will be due on Friday.
Assignment for Friday 10/11
- Try to go through Computerlab Assignment #6 - Use the demo file (here) if you have problems with the server (note if you do this from home, you need to use vpn to get into the cluster (see class 7 fro links to install a vpn client).
- Complete Take Home Exam #4.
Assignment for Monday 10/14
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Class 13
Goals:
- Know about the debates concerning the hot origins of life.
- Understand the arguments for the domain ancestors being survivors of a catastrophe (impact?) that selected to thermophyly
- Understand endosymbiosis and serial endosymbiosis
- Understand the relationship between cheating and division of labor
- Evolution - gradual or with jumps?
- Molecular evolution as a tool to understand disease
- Sequence alignments
Links:
Slides on the late heavy bombardment
Class13.html Class13.pptx
Assignment for Friday 10/11
- Try to go through Computerlab Assignment #6 - Use the demofile (below) if you have problems with the server.
- Complete Take Home Exam #4.
Assignment for Monday 10/14
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Goals Comp Lab 7:
Become familiar with
- the commandline,
- making searchable libraries from multiple sequence files
- running blast,
- simple commands (cat xxx yyy > zzz) and
- scripts to modify files and to parse and plot blast search results
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Class 14
- Review session. Know what to expect on the midterm.
What is the most frequent outcome of a gene duplication?
What is the most frequent outcome, in case the gene doesn't undergon non-functionalization?
What does any of this have to do with building up a post mating hyybrization barrier?
Aside: How can genes be duplicated?
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Goals Comp Lab 8:
- Create gene and mummerplots using the commandline interface.
- Analyze Strand Bias and see its connection to beacterial genome architecture.
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Class 15
Goals
- Know the possible fates of dublicated genes
- Know how gene duplication forllowd by loss of function can lead to a post mating hybridiztion barries.
- Know the differnence between local and global alignments
- Understand how dynamic programming can guarantee an alignment with an optimal alignment score in case of a pairwise alignment.
- Know the advantages and problems of progressive alignment programs.
Assignment for Wednesday 10/22
- Read through the class 15 webpage on sequence alignment
Links:
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Class 16
Goals
- Know how gaps, insertions, repeated domains, and regions of low complexity look like in a dotplot analysis.
- Understand the principle of the progressive alignment approach and the potential downstream problems caused by this analysis.
- Appreciate that multiple sequence alignments can have different goals: pleasing to the human observer; matching sites that in the 3D structure occupy the corresponding location; be certain that alignment columns only contain homologous sites (else align them to gaps).
- Know about different alignment programs (clustalw, Muscle, MAFFT, PRANK)
- Appreciate that the concept of sequence space may be helpful in discussing sequence similarity and evolutionary trajectories
Links:
slides on sequence space
Assignment for Friday 10/25
- Understand the goals and principles of a PCA analysis. Recommended reading materials are here, for much more detailed description and discussion see here
Assignment for Monday 10/28
- Read excerpts of Chapters 5 and 6 from Li's "Molecular Evolution" on HuskyCT
- Try to decide who is correct in the discussion of the Hennigian comb at the bottom of class 16
- Read through the box on introns in class 16
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Goals Comp Lab 9:
- Know how dotlet works, and why this is sometimes advantages over the dot-matrix comparison done in a pairwise blast search.
- Understand the concept of sequence space, and how it may be used or visualize relationships between proteins and to discuss protein evolution.
- Know that a principle component analysis project a multidimensional space onto only a few dimensions.
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Class 17
Goals
- Know about the introns early -introns debate
- Know about the supporting evidence for both sides
- Know how Go plots are created, and how they are used to define protein structure building blocks
- Know why the finding of the intron in TriosePhosphateIsomerase encoding gene Culex is not an arguement for introns early
- Understand the parenthesis or Newick format to denote trees
- Know that swapping brnaches around a node does not change the meaning of a phylogeneitc tree
Links
Assignment for Wednesday 10/30
- Takehome Exam 5 is due
- Work through Olga's example for Bayesian thinking (here)
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Class 18
Goals
- Understand the parenthesis or Newick format to denote trees
- Know the principle behind parsimony analysis and Occam's razor (or Ockham's razor, aka lex parsimoniae)
- Know the similarity and differences between parsimony and maximum likelihood based phylogenetic reconstruction
- Understand the differences between Parismony, Maximum Likelyhood Estimation and Bayesian approaches to phylogneetics.
Links
Assignment for Friday 11/1
Read the slides and the wikipedia entry (Introduction, Distribution, and Example sections) on the maximum likelihood ratio test (https://en.wikipedia.org/wiki/Likelihood-ratio_test)
(also, I found a you tbe video that provides an introduction to the underlying idea at https://www.youtube.com/watch?v=Tn5y2i_MqQ8)
- Read through the slides regarding Maximum Likelyhood, and the ML ratio test
- Try to understand the difference between non-parametric and parametric bootstrapping
Assignment for Monday 11/4
- Go through the Slides on phylogenetic reconstruction
Assignment for Wednesday 11/6
Explore the population genetic simulations at http://www.radford.edu/~rsheehy/Gen_flash/popgen/ (you need to enable flash in your browser).
- Using the same fitness and frequency for the A1 and A2 allele, explore the impact of population size on drift (w11:1; w12:1, w22=1)? [use a population size of 100, 500 generations, an initial frequency of .5, 5 populations]
- For the same population size (100), explore settings that reflect balancing selection. (w11:.9; w12:1, w22=.9) Compare these results to the above.
- What happens, if you decrease the population size?
- Using a small initial frequency of allele 1 (freq. of 0.01 in a population of 50, i.e., you have one allele that conveys a 5% fitness advantage) (w11:1; w12:.95, w22=.9). Perform several simulations. Also try a simulation, where you increase the number of populations from the default 5 to 100 (the coloring doesn't work any more, but the overall count on the right hand site is instructive).
What does this suggest for the effectiveness of natural selection?
- Does natural selection acting on a single advantageous allele work better in a large population? To explore this, increase the population size and lower the frequency, so that you still have one beneficial allele in the population? (e.g., to have one beneficial allele in a population of 500 individuals its freq. is 0.001)
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Goals Comp Lab 10:
- Appreciate the long branch attraction artifact as a serious problem in reconstructiong evolutionary history
- Know which approaches to phylogenetic reconstruction are most, and which are less sensitive to LBA
- Know that missing data can cause a problem in phylogenetic reconstruction, especially if the data missing in some sequences evolve under a different substitution rate
- Know how to test for an appropriate modelto analyse your data
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Class 19
Goals
- Understand the principle behind the Metroplis Coupled Markov Chain Monte Carlo approach to biased sampling in Bayesian exploration of parameter space.
- Understand that the shape parameter of the Gamma distribution allows to estimate the distribution of rate variation along a sequence.
- Know how
- lack of resolution,
- lineage sorting,
- gene transfer,
- introgression, and
- systematic artifacts
- can lead to differences between gene and "species" trees.
Links
Slides on Bayesian approaches, MCMCMC, why are trees different
Assignment for Wednesday 11/6
Explore the population genetic simulations at http://www.radford.edu/~rsheehy/Gen_flash/popgen/ (you need to enable flash in your browser).
- Using the same fitness and frequency for the A1 and A2 allele, explore the impact of population size on drift (w11:1; w12:1, w22=1)? [use a population size of 100, 500 generations, an initial frequency of .5, 5 populations]
- For the same population size (100), explore settings that reflect balancing selection. (w11:.9; w12:1, w22=.9) Compare these results to the above.
- What happens, if you decrease the population size?
- Using a small initial frequency of allele 1 (freq. of 0.01 in a population of 50, i.e., you have one allele that conveys a 5% fitness advantage) (w11:1; w12:.95, w22=.9). Perform several simulations. Also try a simulation, where you increase the number of populations from the default 5 to 100 (the coloring doesn't work any more, but the overall count on the right hand site is instructive).
What does this suggest for the effectiveness of natural selection?
- Does natural selection acting on a single advantageous allele work better in a large population? To explore this, increase the population size and lower the frequency, so that you still have one beneficial allele in the population? (e.g., to have one beneficial allele in a population of 500 individuals its freq. is 0.001)
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Class 20
Goals
- Know the difference between mutation and substitution.
- Understand why for neutral mutations the mutation rate equals the substitution rate.
- Understand that even with very large populations, most mutations that provide a small selective advantage go extinct due to genetic drift.
- Understand how population size impacts the time it takes for fixation of a neutral mutation
- Know what the terms positive, negative, and neutral selection mean and what frequent synonyms for these terms are.
Links:
slides on population genetics, genetic drift , box on page for class 20.
Assignment for Monday 11/11
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Goals Comp Lab 11:
- Appreciate the power of scripts to run programs repeatedly using different input files
- Appreciate the power of scripts to extract information from the verbose output of a program
- Know how simple statistics on all protein sequences present in a genome can inform on the physiology and adaptations of an organism
- Know that analysis of the genome wide composistion of proteins can provide information on optimal growth temperature and adaptation to growth at high salt concentrations.
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Class 21
Goals:
- Know what the terms positive, negative, and neutral selection mean and what frequent synonyms for these terms are.
- Be able to discuss the terms positive and diversifying selection
- Know about the parameters in Ziheng Yang's model to incorporate dN/dS into sequence evolution
- Know that the dN/dS>1 approach can be used to detect positive selection and that this approach is often difficult to apply in case the alignment is unreliable (which results in more non-synonymous substitutions).
- Know that dN/dS <1 reflects that non-synonymous substitutions in this protein lower the fitness.
Links
Assignment for Wednesday
Assignment for Friday
- Refresh you knowledge of Baysian approaches to phylogenetic inference.
Read the following sections in the Wikipedia entry http://en.wikipedia.org/wiki/Bayesian_inference_in_phylogeny: Intro, Bayesian Inference of Phylogeny, Background and Bases , Pitfalls and controversies, MRBAYES software for Bayesian Inference of Phylogeny
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Class 22
Goals:
- Know how to infer the type of selection using synonymous and non-synonymous substitutions.
- Know that one can infer the type of selection from the rate with which a gene goes to fixation.
- Know that the dN/dS>1 approach can be used to detect positive selection and that this approach is often difficult to apply in case the alignment is unreliable (which results in more non-synonymous substitutions).
Links
Assignment for Friday
- Refresh you knowledge of Baysian approaches to phylogenetic inference.
Read the following sections in the Wikipedia entry http://en.wikipedia.org/wiki/Bayesian_inference_in_phylogeny: Intro, Bayesian Inference of Phylogeny, Background and Bases , Pitfalls and controversies, MRBAYES software for Bayesian Inference of Phylogeny
- Complete Take Home Exam #7
Assignment for Monday
- Check out Take Home Exam #8
- Go through the correct answers of exams 5 & 6, discuss in class or the discussion board, if you are not sure why something is correct.
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Goals Comp Lab 12:
- Know about the sump and sumt commands
- Understand why the burnin should be excluded from the analysis
- Know how to read the bipartition tables and trees created by the sumt command
- Know hoy to evaluate the p-files with rescect to high probability intervalls for parameters
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Class 23
Goals:
- Be aware that mutation bias converts more GC pairs into AT pairs than the other way around.
- Know that diversifying selection acts on sites in virus genomes that are recognized by the immune system
- Understand the selection can act on different levels
- Know that ASRV is more extreme for proteins that are under strong purifying selection.
- Know that dN/dS <1 reflects that non-synonymous substitutions in this protein lower the fitness. This does not necessarily imply the gene before the mutation made a positive contribution to the fitness. It only means that the fitness afterwards is lower.
- Know that the absence of SNPs in an allele (or surrounding an allele) can be caused by a selective sweep that erases the diversity around the site being selected for.
Links
Assignment for Wednesday
Assignment for Friday
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Class 24
Goals:
- Know that PSIblast lowers the frequency of false negatives as compared to a normal blast search
- Know the underlying principle of the iteration in PSI blast
- Know what PSI and PSSM stand for
- Understnad what PSI blast and Hmmer searches might be used for
- Be aware that making a PSSM and using it for a search can use different databases.
- Be able to discuss the problems/controversies around the brain size determining genes
Links
Assignment for Friday
Assignment for Monday
- read the Wallstreet Journal on Bruce Lahn (huskyCT reading materials)
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Goals Comp Lab 12:
- Be able to perform PSIblast searches using the web and the command line interface
- Appreciate the differences between blastp, psibast, and using tblastn with a PSSM
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Class 25
- Understand why Constructive Neutral Evolution leads to an increase of complexity.
- Know the arguements for and against the early evolution of life taking place at high / very high temperatures.
Links
Assignment for Wednesday
- Review the slides for class 25
- Fill out SET survey
- Review this page and bring questions for review session.
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