ArticlePloS one2014
FANSe2: a robust and cost-efficient alignment tool for quantitative next-generation sequencing applications.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed.
- Retinal Amyloid Clearance Enhanced by 40-Hz Light Flicker via MHC-II+ Microglia Regulation in Mice.Investigative ophthalmology & visual science · 2026Article
- Plasmid pHXY0908 confers ciprofloxacin heteroresistance to Salmonella enterica serovar typhimurium ATCC 14028 by regulating efflux pump gene expression.BMC microbiology · 2025Article
- Construction and characteristics of an adjustable biomechanical in vitro corneal stromal model simulating keratoconus pathological features.Materials today. Bio · 2025Article
- The influence of femtosecond laser intrastromal lenticules on the characteristics and maturity in tissue-engineered stem cell-derived retinal pigment epithelium sheets.Stem cell research & therapy · 2025Article
- Mechanisms ofInternational journal of molecular sciences · 2025Article
- Comparative analysis of translatomics and transcriptomics in the longissimus dorsi muscle of Luchuan and Duroc pigs.PloS one · 2025Article
- Circulating exosomal miR-16-5p and let-7e-5p are associated with bladder fibrosis of diabetic cystopathy.Scientific reports · 2024Article
- Article
- Comprehensive analysis of the translatome reveals the relationship between the translational and transcriptional control in high fat diet-induced liver steatosis.RNA biology · 2021Article
- The Ultrafast and Accurate Mapping Algorithm FANSe3: Mapping a Human Whole-Genome Sequencing Dataset Within 30 Minutes.Phenomics (Cham, Switzerland) · 2021Article
- Translatomics Probes Into the Role of Lycopene on Improving Hepatic Steatosis Induced by High-Fat Diet.Frontiers in nutrition · 2021Article
- Integrated Transcriptomic and Translatomic Inquiry of the Role of Betaine on Lipid Metabolic Dysregulation Induced by a High-Fat Diet.Frontiers in nutrition · 2021Article
- Mechanotransduction Regulates Reprogramming Enhancement in Adherent 3D Keratocyte Cultures.Frontiers in bioengineering and biotechnology · 2021Article
- Germline variation networks in the PI3K/AKT pathway corresponding to familial high-incidence lung cancer pedigrees.BMC cancer · 2020Article
- Exosome-Derived MiRNAs as Biomarkers of the Development and Progression of Intracranial Aneurysms.Journal of atherosclerosis and thrombosis · 2020Article
- Plasma extracellular vesicle‑packaged microRNAs as candidate diagnostic biomarkers for early‑stage breast cancer.Molecular medicine reports · 2019Article
- A hidden human proteome encoded by 'non-coding' genes.Nucleic acids research · 2019Article
- Misassembly of long reads undermines de novo-assembled ethnicity-specific genomes: validation in a Chinese Han population.Human genetics · 2019Article
- Translatomics: The Global View of Translation.International journal of molecular sciences · 2019Review
- PERK/eIF-2α/CHOP Pathway Dependent ROS Generation Mediates Butein-induced Non-small-cell Lung Cancer Apoptosis and G2/M Phase Arrest.International journal of biological sciences · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Correct and bias-free interpretation of the deep sequencing data is inevitably dependent on the complete mapping of all mappable reads to the reference sequence, especially for quantitative RNA-seq applications. Seed-based algorithms are generally slow but robust, while Burrows-Wheeler Transform (BWT) based algorithms are fast but less robust. To have both advantages, we developed an algorithm FANSe2 with iterative mapping strategy based on the statistics of real-world sequencing error distribution to substantially accelerate the mapping without compromising the accuracy. Its sensitivity and accuracy are higher than the BWT-based algorithms in the tests using both prokaryotic and eukaryotic sequencing datasets. The gene identification results of FANSe2 is experimentally validated, while the previous algorithms have false positives and false negatives. FANSe2 showed remarkably better consistency to the microarray than most other algorithms in terms of gene expression quantifications. We implemented a scalable and almost maintenance-free parallelization method that can utilize the computational power of multiple office computers, a novel feature not present in any other mainstream algorithm. With three normal office computers, we demonstrated that FANSe2 mapped an RNA-seq dataset generated from an entire Illunima HiSeq 2000 flowcell (8 lanes, 608 M reads) to masked human genome within 4.1 hours with higher sensitivity than Bowtie/Bowtie2. FANSe2 thus provides robust accuracy, full indel sensitivity, fast speed, versatile compatibility and economical computational utilization, making it a useful and practical tool for deep sequencing applications. FANSe2 is freely available at http://bioinformatics.jnu.edu.cn/software/fanse2/.
Indexed as
Identifiers
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.