Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Improved representation of sequence Bloom trees

Robert S. Harris, Paul Medvedev
doi: https://doi.org/10.1101/501452
Robert S. Harris
1Department of Biology, The Pennsylvania State University, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Paul Medvedev
1Department of Biology, The Pennsylvania State University, USA
2Department of Computer Science and Engineering, The Pennsylvania State University, USA
3Department of Biochemistry and Molecular Biology, The Pennsylvania State University, USA
4Center for Computational Biology and Bioinformatics, The Pennsylvania State University, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: pashadag@cse.psu.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Motivation Algorithmic solutions to index and search biological databases are a fundamental part of bioinformatics, providing underlying components to many end-user tools. Inexpensive next generation sequencing has filled publicly available databases such as the Sequence Read Archive beyond the capacity of traditional indexing methods. Recently, the Sequence Bloom Tree (SBT) and its derivatives were proposed as a way to efficiently index such data for queries about transcript presence.

Results We build on the SBT framework to construct the HowDe-SBT data structure, which uses a novel partitioning of information to reduce the construction and query time as well as the size of the index. Compared to previous SBT methods, on real RNA-seq data, HowDe-SBT can construct the index in less than 36% of the time, and with 39% less space, and can answer small-batch queries at least five times faster. We also develop a theoretical framework in which we can analyze and bound the space and query performance of HowDe-SBT compared to other SBT methods.

Availability and implementation HowDe-SBT is available as a free open source program on https://github.com/medvedevgroup/HowDeSBT.

Contact Paul Medvedev, pzm11{at}psu.edu

Supplementary information Supplementary text and figures available as single Supplementary file.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
Back to top
PreviousNext
Posted August 15, 2019.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Improved representation of sequence Bloom trees
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Improved representation of sequence Bloom trees
Robert S. Harris, Paul Medvedev
bioRxiv 501452; doi: https://doi.org/10.1101/501452
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Improved representation of sequence Bloom trees
Robert S. Harris, Paul Medvedev
bioRxiv 501452; doi: https://doi.org/10.1101/501452

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3514)
  • Biochemistry (7371)
  • Bioengineering (5347)
  • Bioinformatics (20329)
  • Biophysics (10048)
  • Cancer Biology (7781)
  • Cell Biology (11353)
  • Clinical Trials (138)
  • Developmental Biology (6454)
  • Ecology (9985)
  • Epidemiology (2065)
  • Evolutionary Biology (13361)
  • Genetics (9377)
  • Genomics (12616)
  • Immunology (7729)
  • Microbiology (19119)
  • Molecular Biology (7478)
  • Neuroscience (41163)
  • Paleontology (301)
  • Pathology (1235)
  • Pharmacology and Toxicology (2142)
  • Physiology (3183)
  • Plant Biology (6885)
  • Scientific Communication and Education (1276)
  • Synthetic Biology (1900)
  • Systems Biology (5329)
  • Zoology (1091)