RNA-seq data is currently underutilized, in part because it is difficult to predict the functional impact of alternate transcription events. Recent software improvements in full-length transcript deconvolution prompted researchers from the University of Copenhagen to develop spliceR, an R package ...
Read More »Benchmarks of the read aligner segemehl in comparison with other state-of-the-art methods
Next generation sequencing has become an important tool in molecular biology. Various protocols to investigate genomic, transcriptomic, and epigenomic features across virtually all species and tissues have been devised. For most of these experiments, one of the first crucial steps ...
Read More »Veridical – Validation of predicted mRNA splicing mutations using high-throughput transcriptome data
Interpretation of variants present in complete genomes or exomes reveals numerous sequence changes, only a fraction of which are likely to be pathogenic. Mutations have been traditionally inferred from allele frequencies and inheritance patterns in such data. Variants predicted to ...
Read More »Methods for Analysis of RNA-Seq Datasets to Study Alternative Splicing
Alternative splicing is an important gene regulatory mechanism that dramatically increases the complexity of the proteome. However, how alternative splicing is regulated and how transcription and splicing are coordinated are still poorly understood, and functions of transcript isoforms have been ...
Read More »FineSplice – enhanced splice junction detection and quantification
Alternative splicing is the main mechanism governing protein diversity. The recent developments in RNA-Seq technology have enabled the study of the global impact and regulation of this biological process. However, the lack of standardized protocols constitutes a major bottleneck in ...
Read More »Methods to study splicing from high-throughput RNA sequencing data
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a ...
Read More »SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing
SeqGSEA is an open-source Bioconductor package, for the functional integration of differential expression and splicing analysis in RNA-Seq data. SeqGSEA implements an analysis pipeline which first computes differential splicing (DS) and differential expression (DE) scores, followed by integrating them into ...
Read More »A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection
Numerous high-throughput sequencing studies focus on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through gene fusion, circularization, or trans-splicing are often neglected. Researchers from the University Leipzig, Germany introduce a novel, unbiased algorithm to detect splice ...
Read More »Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data
Point mutations in intronic regions near mRNA splice junctions can affect the splicing process. To identify novel splicing variants from exome sequencing data, researchers at University of Milano–Bicocca, Italy developed a bioinformatics splice-site prediction procedure to analyze next-generation sequencing (NGS) ...
Read More »The Most Informative Spacing Test Effectively Discovers Biologically Relevant Outliers or Multiple Modes in Expression.
Several outlier and subgroup identification statistics (OASIS) have been proposed to discover transcriptomic features with outliers or multiple modes in expression that are indicative of distinct biological processes or subgroups. Here, researchers from the St. Jude Children’s Research Hospital, Memphis borrow ...
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