research-article

Binary Interval Search

Authors:

Aaron R. QuinlanAuthors Info & Claims

Bioinformatics, Volume 29, Issue 1

Pages 1 - 7

https://doi.org/10.1093/bioinformatics/bts652

Published: 01 January 2013 Publication History

Abstract

Motivation: The comparison of diverse genomic datasets is fundamental to understand genome biology. Researchers must explore many large datasets of genome intervals (e.g. genes, sequence alignments) to place their experimental results in a broader context and to make new discoveries. Relationships between genomic datasets are typically measured by identifying intervals that intersect, that is, they overlap and thus share a common genome interval. Given the continued advances in DNA sequencing technologies, efficient methods for measuring statistically significant relationships between many sets of genomic features are crucial for future discovery.

Results: We introduce the Binary Interval Search (BITS) algorithm, a novel and scalable approach to interval set intersection. We demonstrate that BITS outperforms existing methods at counting interval intersections. Moreover, we show that BITS is intrinsically suited to parallel computing architectures, such as graphics processing units by illustrating its utility for efficient Monte Carlo simulations measuring the significance of relationships between sets of genomic intervals.

Availability: https://github.com/arq5x/bits.

Contact: [email protected]

Supplementary information: Supplementary data are available at Bioinformatics online.

Cited By

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Marzolla MBirolo GD’Angelo GFariselli P(2024)Parallel intersection counting on shared-memory multiprocessors and GPUsFuture Generation Computer Systems10.1016/j.future.2024.05.039159:C(423-431)Online publication date: 1-Oct-2024
https://dl.acm.org/doi/10.1016/j.future.2024.05.039
Louri A(2018)Editorial from the Incoming Editor-in-ChiefIEEE Transactions on Computers10.1109/TC.2018.287942168:1(3-3)Online publication date: 10-Dec-2018
https://dl.acm.org/doi/10.1109/TC.2018.2879421
Gulino AKaitoua ACeri S(2018)Optimal Binning for GenomicsIEEE Transactions on Computers10.1109/TC.2018.285488068:1(125-138)Online publication date: 10-Dec-2018
https://dl.acm.org/doi/10.1109/TC.2018.2854880
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Index Terms

Binary Interval Search
1. Applied computing
  1. Life and medical sciences
2. Theory of computation
  1. Design and analysis of algorithms
    1. Approximation algorithms analysis
      1. Scheduling algorithms
  2. Theory and algorithms for application domains
    1. Machine learning theory
      1. Reinforcement learning
        Sequential decision making

Index terms have been assigned to the content through auto-classification.

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Published In

Bioinformatics Volume 29, Issue 1

January 2013

147 pages

ISSN:1367-4803

Issue’s Table of Contents

Publisher

Oxford University Press, Inc.

United States

Publication History

Published: 01 January 2013

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Marzolla MBirolo GD’Angelo GFariselli P(2024)Parallel intersection counting on shared-memory multiprocessors and GPUsFuture Generation Computer Systems10.1016/j.future.2024.05.039159:C(423-431)Online publication date: 1-Oct-2024
https://dl.acm.org/doi/10.1016/j.future.2024.05.039
Louri A(2018)Editorial from the Incoming Editor-in-ChiefIEEE Transactions on Computers10.1109/TC.2018.287942168:1(3-3)Online publication date: 10-Dec-2018
https://dl.acm.org/doi/10.1109/TC.2018.2879421
Gulino AKaitoua ACeri S(2018)Optimal Binning for GenomicsIEEE Transactions on Computers10.1109/TC.2018.285488068:1(125-138)Online publication date: 10-Dec-2018
https://dl.acm.org/doi/10.1109/TC.2018.2854880
Seok HSong TKong SHwang K(2015)An efficient search algorithm for finding genomic-range overlaps based on the maximum range lengthIEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)10.1109/TCBB.2014.236904212:4(778-784)Online publication date: 1-Jul-2015
https://dl.acm.org/doi/10.1109/TCBB.2014.2369042
Marzolla MD'Angelo GMandrioli M(2013)A Parallel Data Distribution Management AlgorithmProceedings of the 2013 IEEE/ACM 17th International Symposium on Distributed Simulation and Real Time Applications10.1109/DS-RT.2013.23(145-152)Online publication date: 30-Oct-2013
https://dl.acm.org/doi/10.1109/DS-RT.2013.23

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PSI-Search

siRNA off-target search: a hybrid q-gram based filtering approach

Homology search for genes

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