The Construction Algorithm

1.

Initialize a contig set, so that for each clone there is a corresponding contig consisting of that clone.

2.

Calculate P_x,y⁺, and |S_x,y(a,b)| for each pair a,b of contigs.

3.

Calculate for all the initial contig pairs and for the two possible relative orientations their relative placement probabilities vector. The results are stored in a table.

4.

Find for all contig pairs and for their two possible relative orientations their best relative placement, and its probability.

5.

While more than one contig remains:
(a) Find two contigs a,b which have relative orientation and placement that attain the highest probability.
(b) Merge b into a.
(c) Change the table calculated in step 3 to reflect the last merger. Only the table entries for all contig pairs (a,c) need to be changed. The required change is a simple combination of the previous entries for (a,c) and for (b,c).
(d) Find, for contig pairs affected by the merger, their new best relative placement.

Assume that there are n probes and m clones of length d, and the genome has length L. The bottleneck steps in the computation are:

• Step 2 that takes O(m²n) time.
• Steps 3-4 that take O(m²d) time
• Steps 5(c) and 5(d) that take O(mL) time.

Step 5 is repeated m-1 times giving a total complexity of O(m²(L+d+n)).