title: A novel partial sequence alignment tool for finding large deletions.
abstract: 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.
authors.affiliation: Scientific and Technological Research Council of Turkey (TUBITAK), 41470 Kocaeli, Turkey.
authors.forename: Taner
authors.initials: T
authors.lastname: Aruk
authors.forename: Duran
authors.initials: D
authors.lastname: Ustek
authors.forename: Olcay
authors.initials: O
authors.lastname: Kursun
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D004272:DNA, Mitochondrial / Q000235:genetics*; D020407:Internet; D008928:Mitochondria / Q000235:genetics; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D017384:Sequence Deletion; D012984:Software
chemical_list: D004272:DNA, Mitochondrial