mathematically speaking,
suppose you have the two mappings a:{1,..,n}>{A,C,G,T} and b:{1,..,m}>{A,C,G,T}
representing the two genomes.
pick L (e.g. L=16) and compute
f:{1,..,nL}>{0,1}
with
f(x)=1, iff exists y such that a(x+i)=b(y+i) , i=0..L1
this can quickly be computed by marking all values of b in a 4^L table.
[you may add the inverse complement of b() here]
then plot moving averages of f, the number of values in the averages being
approximately the length of the expected gene.
this gives an overview of the matchingquality by genomeregion
you should see a "valley" in a nonmatching region
[is there a name for this function ?]
