. The function o.lap (which can be downloaded from http://www. cmb.usc.edu) constructs the portion of an overlap matrix resulting from comparing direct reads rk and rl with each other, recording any...

.
The function o.lap (which can be downloaded from http://www.

cmb.usc.edu) constructs the portion of an overlap matrix resulting from comparing

direct reads rk and rl with each other, recording any matches below

the diagonal of the overlap matrix.

a. Modify this function so that it will create the portion of the overlap matrix

above the diagonal, corresponding to alignment of direct reads rk to

complementary reads r∗

l .

b. The code fragment

#test for overlap of j with left end of i

s<-0>

for(q in 0:(m-1)){

if(inseq[j,(k+q)]==le[q+1])

{s

...

does not impose a penalty for mismatches when computing score s. Is a

mismatch penalty needed in this application? Why or why not?