A Novel Partial Sequence Alignment Tool for Finding Large Deletions

Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method

A Comparative Analysis of Smith-Waterman Based Partial Alignment

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

A Novel Partial Sequence Alignment Tool for Finding Large Deletions

Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straightforward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method