MO640 - Exercises - SCJ Distances and Medians, Feijao and Meidanis 2011

Exercises marked with (*) require further reading/search beyond the suggested texts.

1. Compute the SCJ distance between the following genomes:

Answer:

If E is the set of adjacents from the first genome and R is the set of adjacents from the second genome, the SCJ distance is:

D_SCJ(E,R) = | E - R | + | E - R |
D_SCJ(E,R) = 5 + 5
D_SCJ(E,R) = 10.

because

E - R = { ND3_hND4L_t, ND5_hND6_h, ND6_tCytB_t, CYTB_h12S_t, ND1_hND2_t }
R - E = { ND3_hND5_h, ND4L_tND6_t, ND6_hCytB_t, CYTB_hND1_h, 12S_tND2_t }