Splicing and Junction Mapping

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Kleat – cleavage site analysis of transcriptomes

Kleat – cleavage site analysis of transcriptomes

In eukaryotic cells, alternative cleavage of 3′ untranslated regions (UTRs) can affect transcript stability, transport and translation. For polyadenylated (poly(A)) transcripts, cleavage sites can be characterized with short-read sequencing using specialized library construction methods. However, for large-scale cohort studies as ...

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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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