Read the summary and the most important questions on Algorithms in Sequence Analysis

• 1 Intro + Pairwise alignment

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• What does sequence analysis exploit?

  Patterns arising during evolution. 
  

  • Specifically: during divergent evolution, starting at a common origin, leading to discernible similarity (conservation patterns) in many cases. 
  • * Patterns are not uniformely tractable, since different selective pressures lead to very different degrees of conservation of features, due to functional constraints 

• Which 3 components of the human exposome did Wild describe?

  • A general external environment including urban environment, climate factors, education, social capital and stress.
    
  • A specific external environment with specific contaminants, radiation, infection, lifestyle factors, diet, physical activity etc.
  • An internal environment including internal biological factors such as metabolic factors, hormones, gut microbiome, inflammation, oxidative stress.

• Homolgy means common ancestry. So homologous genes have a common ancestor. There are two forms of homology. Explain.

  1. Orthology: orthologous genes are homologous genes in different species (genomes) relating to the speciation event. 
  2. Paralogy: Paralogous genes are homologous genes (repeats) within the same species (genome)

• What is meant by Burst after Duplication? (BAD)

  After a gene duplication, the selection pressure is low on this region. Therefore, mutations and genetic drift can increase. 
  
  A related phenomenon is adaptive radiation: a process in which organisms diversify rapidly into a multitude of new forms, particulary when a change in the environment makes new resources available, creates new challenges and opens environmental niches.

• What is horizontal gene transfer? (xenology)

  • Also called lateral gene transfer
    
  • Occurs when organisms incorporates genetic material from other organism without being the offspring of that organism.
  • (receiving material from ancestor = vertical transfer)
  • Most thinking in genetics has focussed on vertical transfer but increasing awareness of horizontal transfer.
  • Artificial horizontal gene transfer is form of genetic engineering.

• What are transitions and transversions?

  Mutation type. 
  
  We have purines and pyrimidines:
  

  • A & G = purine
  • C & T/U = pyrimidine

  
  Transition:
  

  • purine to purine
  • pyrimidine to purine

  Transversion:
  

  • purine to pyrimidine
  • pyrimidine to purine

• What is a synonymous mutation? And a non-synonymous one?

  • Synonymous: mutation that does not lead to an amino acid change
    
  • Non-synonymous mutation: mutation that does lead to an amino acid change
  • missense mutation: one aa replaced by other aa
  • nonsense mutation: aa replaced by stopcodon

• Many proteins consist of repeats. Sometimes to gain function, sometimes leading to disease (eg single residue repeats). Name some features.

  • Evolution reuses developed material. 
    
  • Multiple stochiometric and spatially close combined structure function relationships
  • In proteins, repeats vary from a single aa to complete domains
  • Many types of (near) identical repeats exist in genomes. Human genome > 50%.
  • eg DNA transposons

• What is a transposon?

  Also: "springend gen". One or multiple genes, with small sequences (Insertion sequences)(inverted in respect to one another) on both sides and a gene for transposition. Insertion sequences contain no information. 
  
  Transposase enzyme binds to both IS, and to the location in DNA where it should go. Cuts DNA. Sticky ends are completed again. Some transposons require specific site, others can go everywhere.

• What is meant by the structure/function gap?

  There are far more sequences than solved tertiary structures and functional annotations. This gap is growing, so there is a need to predict structure and function.