Similarity vs. Homology

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Similarity vs. Homology
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Homology defined

• "The same organ in different animals under a
  variety of form and function.
• Sir Richard Owen, Lectures on the Comparative
  Anatomy and Physiology of the Invertebrate
  Animals, 1843.

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Homology defined - 2

• "The mechanism of homology is heredity.
• Allan Boyden, Homology and Analogy A century
  after the definitions of "homologue" and
  "analogue" of Richard Owen,1943.

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Anatomical Homology
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Homology defined - 3

• "Homology is a relation bearing on recency of
  common ancestry.
• Olivier Rieppel, Homology and Logical Fallacy,
  1992.

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A working definition

• Structures or organs which share a common
  ancestor are homologous.

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Sharing a Common AncestorOrthology
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Orthologs Hemoglobin A
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Sharing a Common AncestorParalogy
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• Paralogs F-1 ATP Synthase (energy conversion)
  and Transcription Termination Factor Rho (shuts
  off transcription in E. coli)

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Functional Conservation

• Biochemical Function What protein does on a
  biochemical level, almost always conserved
  between homologs.
• Example Serine/ Threonine Kinase

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Functional Conservation

• Physiological Function What role protein plays
  within the organism, only conserved for
  orthologous proteins.
• Example Glycogen Synthase Kinase

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Sequence Evolution

• Homologs sequences derived from common ancestor.
• DNA sequences strings of four characters.
• Sequence analysis has revealed certain mutational
  regularities.
• Closely-related transitions/transversions
• Distantly-related amino acid mutations.
• We can use these mutational regularities to help
  us identify distantly-related sequences that we
  would not recognize by visual examination alone.

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Homology Detection Strategy

• Compare sequence of interest ("query") to a
  database of known sequences.
• Tabulate all similarity scores.
• Fit scores to a known distribution to detect
  scores that are significantly greater than the
  mean.

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Inferring Physiological Function from Homology