Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

3.3K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
3.3K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.8K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Genome misassembly detection using Stash: A data structure based on stochastic tile hashing.

PloS one·2026
Same author

Bloom Syndrome Presenting With Early-Onset Myelodysplastic Syndrome and Triple Overlapping Vascular Neurocutaneous Phenotypes: A Case Report.

Clinical case reports·2026
Same author

A Systematic Review of Literature: TNF-α Blockers and JAK Inhibitors for the Treatment of Stevens-Johnson Syndrome, Toxic Epidermal Necrolysis, and Severe Forms of Erythema Multiforme.

Health science reports·2026
Same author

Decoding phage communication: molecular networks, evolutionary dynamics, and therapeutic applications.

NPJ biofilms and microbiomes·2026
Same author

Genome annotation of <i>Microbacterium</i> phage Statler containing a putative anti-CBASS gene (Acb2).

Microbiology resource announcements·2026
Same author

Efficacy and safety evaluation of artificial intelligence-identified antimicrobial peptides targeting avian pathogenic Escherichia coli in broiler chickens.

Journal of animal science and biotechnology·2026

Related Experiment Video

Updated: Apr 25, 2026

Isolation, Propagation, and Identification of Bacterial Species with Hydrocarbon Metabolizing Properties from Aquatic Habitats
10:03

Isolation, Propagation, and Identification of Bacterial Species with Hydrocarbon Metabolizing Properties from Aquatic Habitats

Published on: December 7, 2021

5.4K

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.

Justin Chu1, Sara Sadeghi1, Anthony Raymond1

  • 1Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada.

Bioinformatics (Oxford, England)
|August 22, 2014
PubMed
Summary

BioBloom Tools efficiently screens large biological sequence datasets using Bloom filters. This novel tool offers fast, memory-efficient sequence identification with controlled false positives.

More Related Videos

Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health
08:36

Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health

Published on: October 9, 2017

9.4K
A Highly Scalable Approach to Perform Ecological Surveys of Selfing Caenorhabditis Nematodes
09:10

A Highly Scalable Approach to Perform Ecological Surveys of Selfing Caenorhabditis Nematodes

Published on: March 1, 2022

3.0K

Related Experiment Videos

Last Updated: Apr 25, 2026

Isolation, Propagation, and Identification of Bacterial Species with Hydrocarbon Metabolizing Properties from Aquatic Habitats
10:03

Isolation, Propagation, and Identification of Bacterial Species with Hydrocarbon Metabolizing Properties from Aquatic Habitats

Published on: December 7, 2021

5.4K
Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health
08:36

Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health

Published on: October 9, 2017

9.4K
A Highly Scalable Approach to Perform Ecological Surveys of Selfing Caenorhabditis Nematodes
09:10

A Highly Scalable Approach to Perform Ecological Surveys of Selfing Caenorhabditis Nematodes

Published on: March 1, 2022

3.0K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Large-scale biological sequence data analysis requires efficient methods for identifying specific sequences.
  • Traditional sequence alignment algorithms can be computationally intensive and memory-demanding.
  • Bloom filters provide a probabilistic data structure for fast set membership queries but require management of false positives.

Purpose of the Study:

  • To introduce BioBloom Tools, a novel software tool for rapid and memory-efficient screening of large sequence datasets.
  • To evaluate the performance of BioBloom Tools against existing popular sequence analysis tools.
  • To demonstrate the capability of BioBloom Tools in controlling false positives while maintaining high accuracy.

Main Methods:

  • Implementation of a Bloom filter-based data structure for sequence set membership queries.
  • Comparative performance analysis against BWA, Bowtie 2, and FACS using key metrics like speed and memory usage.
  • Assessment of accuracy and false positive rates in sequence screening tasks.

Main Results:

  • BioBloom Tools significantly outperforms BWA, Bowtie 2, and FACS in terms of speed and memory efficiency.
  • The tool achieves accuracies comparable to established alignment algorithms.
  • Effective control over false positives was demonstrated, ensuring reliable screening results.
  • Low memory requirements make BioBloom Tools suitable for resource-constrained environments.

Conclusions:

  • BioBloom Tools offers a superior solution for large-scale sequence screening, balancing speed, memory efficiency, and accuracy.
  • The Bloom filter-based approach provides a viable and effective alternative to traditional alignment algorithms for specific bioinformatics tasks.
  • This tool enhances the capability for rapid identification of organism-specific sequences within massive datasets.