A Novel Partial Sequence Alignment Tool for Finding Large Deletions

Figure 2

Failure of the classical Smith-Waterman alignment in detecting the large deletion at base position 27. In this simulated experiment, the former part is actually known to be the first 27 nucleotides printed in blue in the “Query pattern”. In “Alignment result”, bases shown in red do actually belong to the latter part but were aligned together with the nucleotides of the former part of the query. SW gives the deletion position estimate of 37, which results in an EDPE of 10 bp.