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/
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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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