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What is the longest match between the human and chimpanzee genomes?

May 17, 2024 | Science


Human-chimpanzee similarity is a hotly-debated topic in the evolution-creation wars. Are we 98, 95, 90, or 85% similar? One way to get at the question is to ask what is the longest stretch of DNA that is shared between the two species. This is a very difficult question to answer! But, unperturbed, Dr Rob set out to answer it. Will our fearless hero be able to pull it off? Spoiler alert: not quite, but the path of discovery is still very interesting.

  • LastZ github.com/lastz/lastz
  • LastZ chaining github.com/hillerlab/make_lastz_chains
  • Mummer4 mummer4.github.io/
  • Blast blast.ncbi.nlm.nih.gov/Blast.cgi
  • Telomere-to-Telomere Consortium primate projects github.com/marbl/Primates
  • Python python.org/
  • Standard Bases:

    • A: Adenine
    • C: Cytosine
    • G: Guanine
    • T: Thymine (in DNA)
    • U: Uracil (in RNA)

    Ambiguous Bases (IUPAC Codes):

    These codes are used when there is ambiguity in the nucleotide present at a particular position:

    • R: A or G (puRine)
    • Y: C or T (pYrimidine)
    • S: G or C
    • W: A or T (Weak)
    • K: G or T (Keto)
    • M: A or C (aMino)
    • B: C, G, or T (not A) (B comes after A)
    • D: A, G, or T (not C) (D comes after C)
    • H: A, C, or T (not G) (H comes after G)
    • V: A, C, or G (not T) (V comes after U; U is replaced with T in DNA)
    • N: Any base (A, C, G, T) (N for any nucleotide)
  • Silver Comet Trail silvercometga.com/

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