ArticlePloS one2010
HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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
27 citing papers in PubMed.
- Differential expression of mitochondria-associated genes in clinical samples of Plasmodium falciparum showing severe manifestations.BMC genomics · 2026Article
- Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis.World journal of stem cells · 2021Review
- Genetic Diversity and Gene Family Expansions in Members of the Genus Entamoeba.Genome biology and evolution · 2019Article
- A mutually exclusive stem-loop arrangement in roX2 RNA is essential for X-chromosome regulation inGenes & development · 2017Article
- Undiscovered Physiology of Transcript and Protein Networks.Comprehensive Physiology · 2016Review
- SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing.Nucleic acids research · 2015Article
- Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics.Scientific reports · 2015Article
- Survey of Programs Used to Detect Alternative Splicing Isoforms from Deep Sequencing Data In Silico.BioMed research international · 2015Review
- Altered gamma-aminobutyric acid type B receptor subunit 1 splicing in alcoholics.Biological psychiatry · 2014Article
- Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing.PLoS computational biology · 2014Article
- Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum.BMC genomics · 2014Article
- Article
- KSHV 2.0: a comprehensive annotation of the Kaposi's sarcoma-associated herpesvirus genome using next-generation sequencing reveals novel genomic and functional features.PLoS pathogens · 2014Article
- Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster.eLife · 2013Article
- Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity.Current genomics · 2013Article
- TrueSight: a new algorithm for splice junction detection using RNA-seq.Nucleic acids research · 2013Article
- Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica.Nucleic acids research · 2013Article
- Interaction of cyclin-dependent kinase 12/CrkRS with cyclin K1 is required for the phosphorylation of the C-terminal domain of RNA polymerase II.Molecular and cellular biology · 2012Article
- Comparative evaluation of intron prediction methods and detection of plant genome annotation using intron length distributions.Genomics & informatics · 2012Article
- RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.Nucleic acids research · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
backgroundHigh-throughput sequencing of an organism's transcriptome, or RNA-Seq, is a valuable and versatile new strategy for capturing snapshots of gene expression. However, transcriptome sequencing creates a new class of alignment problem: mapping short reads that span exon-exon junctions back to the reference genome, especially in the case where a splice junction is previously unknown. METHODOLOGY/PRINCIPAL
findingsHere we introduce HMMSplicer, an accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets. HMMSplicer identifies more splice junctions than currently available algorithms when tested on publicly available A. thaliana, P. falciparum, and H. sapiens datasets without a reduction in specificity. CONCLUSIONS/SIGNIFICANCE: HMMSplicer was found to perform especially well in compact genomes and on genes with low expression levels, alternative splice isoforms, or non-canonical splice junctions. Because HHMSplicer does not rely on pre-built gene models, the products of inexact splicing are also detected. For H. sapiens, we find 3.6% of 3' splice sites and 1.4% of 5' splice sites are inexact, typically differing by 3 bases in either direction. In addition, HMMSplicer provides a score for every predicted junction allowing the user to set a threshold to tune false positive rates depending on the needs of the experiment. HMMSplicer is implemented in Python. Code and documentation are freely available at http://derisilab.ucsf.edu/software/hmmsplicer.
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.