Class12 --2015

Assignment for Wednesday's class:

Prepare for midterm.

Complete Assignment #6 part 1 (you can leave out the histograms, but you should have a folder in your directory on the cluster that contains the results of a blast search of one genome against a distantly related one (using the *.faa file).

Think about the question how new genes are created, and how genome size can increase. Everyone should have at least three distinct mechanisms.
Read The Evolutionary Fate and Consequences of Duplicate Genes

Questions on commandline blast

Questions re. take home exam #3

Questions regarding midterm.

ELSE

example of what else one could do with this:
- (perl script to extract top scoring hits is here)
- (perl script to replace gi number with position on the genome is here)
- (perl script to make gnuplot is here, output for Thermotoga maritima vs Th. petrophila is here, plots for comparison between different Aeromonas species are here, here and here).
  Discuss: Which recombination events could have created these patterns?

Appreciate that life may be older than the late heavy bombardment.
Know how to adjust significant levels of individual experiments to avoid fishing expeditions.
Know about the problem facing the scientific community through the underreporting of negative results.

Goals class 10

Understand how the databanks at the NCBI are different from flatfile and relational databanks.
Be able to discuss the advantages of the commandline in general and blast searches via the commandline in particular.

Goals class 9:

Distinguish false positives and false negatives, especially with respect to databank searches
Understand the difference between P and E values
Know about usual cut-offs for Z-scores, P- and E-values.
Understand the impact of E-value cutoff in blast
Understand the impact of the low complexity filter in blast

Goals class 8:

Understand how to analyze exponential growth / decay.
Understand the problems that result from ownership of database entries (know a few examples).
Be able to discuss the process that may lead to the decay of significance

Know the differences between Lamarck's and Darwin's theory, mutationism and the modern synthesis.
Understand the power and the limitations of the tree of life image.
Understand that without selection for function, sequences would have diverged beyond recognition.

Understand the different meanings of the term evolution ("As in evolution of the universe" vs "Nothing in biology makes sense if not considered in the light of evolution".
Appreciate the power of natural selection
Understand that other mechanisms in addition to natural selection might be at play in biological evolution

Understand a few different approaches on how life has been defined/characterized.
Be able to discuss how viruses fit into the concepts of life and living things.
Understand that the evolution of Daisyworld does not represent natural selection.
Be able to discuss pros and cons of NASA's definition of life.
Understand the argument that life and inheritance might have preceeded a genetic system based on nucleic acid like molecules.
(no biopolymer life (autocatalytic reaction cycles) -> single biopolymer life ("RNA world") -> two biopolymer life)

Know a few examples for the study of molecular evolution being helpful in other areas of biology.
Understand that different mechanisms (gene duplication, gene transfer, lineage fusion) can lead to many homologs coexisting in a single cell, or even in a single multi subunit enzyme.
Understand how the origin of the recent ebola outbreak has been followed using molecular data.

Understand that RNA can be both genetic material and catalyst
Know what else supports the RNA-world concept
Understand the homology concept used evolutionary biology
Know that most significantly similar complex sequences (in their primary sequence) are homologous, and that not all homologous sequences are significantly similar in a pairwise comparison of the primary sequence.
Know the difference between primary, secondary and tertiary structure
Recognise secondary structure elements
Know that the combinatoric protein space is huge, but highly connected
Be able to explain, how functional proteins might have evolved despite combinatoric protein being huge

Know how to contact the instructor and TA.
Understand how your performance will be assessed and graded.
Understand that the assignments are an important part of this course, and that they will be graded.
Know at least three examples for the connection between bioinformatics and the study of molecular evolution.
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.