ArticleNucleic acids research2013
OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
81 citing papers in PubMed.
- Expanded Polyglycine Protein Aggregates Alter the RNA Splicing Profile into a Premature State Partially via Sequestering SF3B4.Neuroscience bulletin · 2026Article
- Onconeural antigen NOVA1 dysregulates RNA alternative splicing in breast cancer.RNA (New York, N.Y.) · 2026Article
- A neuron type-specific microexon in Ank3/ankyrin-G modulates calcium activity and neuronal excitability.Nature communications · 2026Article
- Primate-specific adaptation of Ku protects transcriptomic integrity by suppressing Alu-mediated alternative splicing.bioRxiv : the preprint server for biology · 2025Article
- A neuron type-specific microexon inbioRxiv : the preprint server for biology · 2025Article
- Transcriptomic analysis reveals lung cancer and subtype-specific alternative splicing biomarkers regulated by RNA-binding proteins.Molecular therapy. Nucleic acids · 2025Article
- Dysregulated RNA-binding proteins and alternative splicing: Emerging roles in autism spectrum disorder.Molecules and cells · 2025Review
- Reverse engineering neuron-type-specific and type-orthogonal splicing-regulatory networks using diverse cellular transcriptomes.Cell reports · 2025Article
- Bioinformatic Analysis of the Protective Effects of Dexmedetomidine and Thrombopoietin Against Hypoxia/Reoxygenation-Induced Injury in AC16 Cells.Chemical biology & drug design · 2025Article
- A humanized NOVA1 splicing factor alters mouse vocal communications.Nature communications · 2025Article
- The E2F4 transcriptional repressor is a key mechanistic regulator of colon cancer resistance tobioRxiv : the preprint server for biology · 2025Article
- NF-κB RelA regulates temporal oligodendrocyte differentiation in the postnatal brains.Frontiers in cellular neuroscience · 2025Article
- Qki5 safeguards spinal motor neuron function by defining the motor neuron-specific transcriptome via pre-mRNA processing.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Regulation of endocrine cell alternative splicing revealed by single-cell RNA sequencing in type 2 diabetes pathogenesis.Communications biology · 2024Article
- Lineage-specific splicing regulation of MAPT gene in the primate brain.Cell genomics · 2024Article
- CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements.Nature communications · 2024Article
- Counting pseudoalignments to novel splicing events.Bioinformatics (Oxford, England) · 2023Article
- Ddx20, an Olig2 binding factor, governs the survival of neural and oligodendrocyte progenitor cells via proper Mdm2 splicing and p53 suppression.Cell death and differentiation · 2022Article
- Isolation and characterization of human embryonic stem cell-derived heart field-specific cardiomyocytes unravels new insights into their transcriptional and electrophysiological profiles.Cardiovascular research · 2022Article
- Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants.Nature communications · 2022Article
21 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not rely on a separate external aligner. It achieves high sensitivity of junction detection by strategic searches with small seeds (~14 nt for mammalian genomes). To improve accuracy and resolve ambiguous mapping at junctions, OLego uses a built-in statistical model to score exon junctions by splice-site strength and intron size. Burrows-Wheeler transform is used in multiple steps of the algorithm to efficiently map seeds, locate junctions and identify small exons. OLego is implemented in C++ with fully multithreaded execution, and allows fast processing of large-scale data. We systematically evaluated the performance of OLego in comparison with published tools using both simulated and real data. OLego demonstrated better sensitivity, higher or comparable accuracy and substantially improved speed. OLego also identified hundreds of novel micro-exons (<30 nt) in the mouse transcriptome, many of which are phylogenetically conserved and can be validated experimentally in vivo. OLego is freely available at http://zhanglab.c2b2.columbia.edu/index.php/OLego.
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What OpenQuestion holds
Registered trials
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.