Working in Matlab I have 2 vectors of x coordinate with different length. For example:
xm = [15 20 24 25 26 35 81 84 93];
xn = [14 22 26 51 55 59 70 75 89 96
Taking advantage of being sorted, as David says, will be faster since you have so many points, but for reference one way to vectorize this would be to use meshgrid:
[X Y] = meshgrid(xn, xm);
diffs = X - y;
mins = min(diffs, [], 2);
Note that this will create two 100,000 x 100,000 arrays in memory, so it's probably only feasible for smaller data sets.