The New Multi-Fragment Ligation feature uses a different algorithm from the conventional Advanced Ligation, which was limited to up to 5 fragments. The following shows an outline of this algorithm.
- Load the GenBank files of N DNA fragments.
- There is no limit on N.
- Build an N×N adjacency matrix (AM).
- Use AM to build a graph of connectable fragments.
- Extract the connected components (ligation products).
- Determine the fragment join order for each ligation product.
- At this point, if the number of products generated exceeds 1,000,000, processing is terminated to avoid wasting resources.
- This completes the simulation stage; the results are shown in the Ligation Table, and a preview of each product's state immediately before ligation is drawn.