Splicing and Junction Mapping

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SNPlice – identify cis-acting, splice-modulating variants from RNA-seq datasets

SNPlice – identify cis-acting, splice-modulating variants from RNA-seq datasets

The growing recognition of the importance of splicing in eukaryotes, together with rapidly accumulating RNA-sequencing data, demand robust high-throughput approaches, which efficiently analyze experimentally derived whole-transcriptome splice profiles. Researchers from The George Washington University have developed a computational approach, called ...

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Strategies for transcriptional splice variant detection

Strategies for transcriptional splice variant detection

The advent and improvement of high-throughput sequencing over the past decade leveraged the study of whole genomes and transcriptomes of different organisms at lower costs. In transcriptomics, RNA-Seq expands our capacity to understand gene expression in different tissues and pathologies, ...

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CLASS – Splice Variant Annotation from RNA-Seq Reads

CLASS – Splice Variant Annotation from RNA-Seq Reads

Next generation sequencing of cellular RNA is making it possible to characterize genes and alternative splicing in unprecedented detail. However, designing bioinformatics tools to capture splicing variation accurately has proven difficult. Current programs find major isoforms of a gene but ...

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Open-access synthetic spike-in mRNA-seq data for cancer gene fusions

Open-access synthetic spike-in mRNA-seq data for cancer gene fusions

Oncogenic fusion genes underlie the mechanism of several common cancers. Next-generation sequencing based RNA-seq analyses have revealed an increasing number of recurrent fusions in a variety of cancers. However, absence of a publicly available gene-fusion focused RNA-seq data impedes comparative ...

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