ArticleJournal of computational biology : a journal of computational molecular cell biology2018
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- K2R: Tinted de Bruijn graphs implementation for efficient read extraction from sequencing datasets.Bioinformatics advances · 2025Article
- Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters.Genome research · 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
- Scalable sequence database search using partitioned aggregated Bloom comb trees.Bioinformatics (Oxford, England) · 2023Article
- KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping.Bioinformatics (Oxford, England) · 2023Article
- Strain level microbial detection and quantification with applications to single cell metagenomics.Nature communications · 2022Article
- 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
- CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices.Bioinformatics (Oxford, England) · 2022Article
- An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation.Bioinformatics (Oxford, England) · 2022Article
- Data Structures to Represent a Set ofACM computing surveys · 2022Article
- Expected 10-anonymity of HyperLogLog sketches for federated queries of clinical data repositories.Bioinformatics (Oxford, England) · 2021Article
- Disk compression of k-mer sets.Algorithms for molecular biology : AMB · 2021Article
- Data structures based onGenome research · 2021Review
- Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs.Genome biology · 2020Article
- To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics.Nucleic acids research · 2020Article
- An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search.Journal of computational biology : a journal of computational molecular cell biology · 2020Article
- Sparse Binary Relation Representations for Genome Graph Annotation.Journal of computational biology : a journal of computational molecular cell biology · 2020Article
- Improved representation of sequence bloom trees.Bioinformatics (Oxford, England) · 2020Article
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2 authors.
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Abstract
Enormous databases of short-read RNA-seq experiments such as the NIH Sequencing Read Archive are now available. These databases could answer many questions about condition-specific expression or population variation, and this resource is only going to grow over time. However, these collections remain difficult to use due to the inability to search for a particular expressed sequence. Although some progress has been made on this problem, it is still not feasible to search collections of hundreds of terabytes of short-read sequencing experiments. We introduce an indexing scheme called split sequence bloom trees (SSBTs) to support sequence-based querying of terabyte scale collections of thousands of short-read sequencing experiments. SSBT is an improvement over the sequence bloom tree (SBT) data structure for the same task. We apply SSBTs to the problem of finding conditions under which query transcripts are expressed. Our experiments are conducted on a set of 2652 publicly available RNA-seq experiments for the breast, blood, and brain tissues. We demonstrate that this SSBT index can be queried for a 1000 nt sequence in <4 minutes using a single thread and can be stored in just 39 GB, a fivefold improvement in search and storage costs compared with SBT.
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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.