ArticleBioinformatics (Oxford, England)2020
Improved representation of sequence bloom trees.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.Nature biotechnology · 2026Article
- A k-mer-based estimator of the substitution rate between repetitive sequences.Algorithms for molecular biology : AMB · 2026Article
- Kaminari: a frugal colored index for approximateBioinformatics advances · 2026Article
- Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.bioRxiv : the preprint server for biology · 2025Article
- A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- The Statistics of Parametrized Syncmers in a Simple Mutation Process Without Spurious Matches.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters.Genome research · 2024Article
- Compression algorithm for colored de Bruijn graphs.Algorithms for molecular biology : AMB · 2024Article
- Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.Nature computational science · 2024Article
- Methods for Pangenomic Core Detection.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Compression Algorithm for Colored de Bruijn Graphs.Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) · 2023Article
- Scalable sequence database search using partitioned aggregated Bloom comb trees.Bioinformatics (Oxford, England) · 2023Article
- Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries.Genome biology · 2023Article
- fimpera: drastic improvement of Approximate Membership Query data-structures with counts.Bioinformatics (Oxford, England) · 2023Article
- MetaProFi: an ultrafast chunked Bloom filter for storing and querying protein and nucleotide sequence data for accurate identification of functionally relevant genetic variants.Bioinformatics (Oxford, England) · 2023Article
- KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping.Bioinformatics (Oxford, England) · 2023Article
- Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments.Bioinformatics (Oxford, England) · 2022Article
- SPRISS: approximating frequent k-mers by sampling reads, and applications.Bioinformatics (Oxford, England) · 2022Article
- An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation.Bioinformatics (Oxford, England) · 2022Article
Corrections and comments
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2 authors.
Funding
Abstract
motivationAlgorithmic 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.
resultsWe 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.