Choosing the best heuristic for seeded alignment of DNA sequences

BMC Bioinformatics
Yanni Sun, Jeremy Buhler

Abstract

Seeded alignment is an important component of algorithms for fast, large-scale DNA similarity search. A good seed matching heuristic can reduce the execution time of genomic-scale sequence comparison without degrading sensitivity. Recently, many types of seed have been proposed to improve on the performance of traditional contiguous seeds as used in, e.g., NCBI BLASTN. Choosing among these seed types, particularly those that use information besides the presence or absence of matching residue pairs, requires practical guidance based on a rigorous comparison, including assessment of sensitivity, specificity, and computational efficiency. This work performs such a comparison, focusing on alignments in DNA outside widely studied coding regions. We compare seeds of several types, including those allowing transition mutations rather than matches at fixed positions, those allowing transitions at arbitrary positions ("BLASTZ" seeds), and those using a more general scoring matrix. For each seed type, we use an extended version of our Mandala seed design software to choose seeds with optimized sensitivity for various levels of specificity. Our results show that, on a test set biased toward alignments of noncoding DNA, transition informat...Continue Reading

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Citations

Dec 2, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jialiang Yang, Louxin Zhang
Feb 3, 2009·Algorithms for Molecular Biology : AMB·Pierre PeterlongoMarie-France Sagot
Feb 5, 2014·Nucleic Acids Research·Martin C Frith, Laurent Noé
May 11, 2007·Annual Review of Genomics and Human Genetics·Mathieu Blanchette
Jul 17, 2020·Frontiers in Genetics·Guillaume J FilionEduard Zorita
Dec 22, 2020·Bioinformatics·Martin C FrithGregory Kucherov

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Software Mentioned

BLASTZ
CHAOS
MathType
BLASTP
YASS
FLASH
BLAST
PatternHunter
SIM
BLAT

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