A novel partial sequence alignment tool for finding large deletions.

TheScientificWorldJournal
Taner ArukOlcay Kursun

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.

References

Aug 1, 1986·The Journal of Pediatrics·R D Schmickel
Mar 25, 1981·Journal of Molecular Biology·T F Smith, M S Waterman
Jan 23, 1999·American Journal of Human Genetics·M V Olson
Aug 9, 2002·Theoretical Population Biology·Dmitri A Petrov
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Dec 6, 2005·Nature Genetics·Donald F ConradJonathan K Pritchard

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Software Mentioned

SSEARCH
IncrementalPartialAlign
Path
NGS
Water
JAligner
UGENE
BinaryPartialAlign
BLOSUM

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