Finding large deletions in genome sequences have become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Several partial alignment approaches based on the Smith-Waterman (SW) algorithm has been proposed for alignment with large gaps. However, in the literature, no detailed comparisons of these three SW-based methods were given in terms of the runtimes and errors in estimated position of the start of the deletion in the query sequences. Our comparative simulations show that BinaryPartialAlign has the lowest error and very high speed.