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/