Advancements in sequencing technologies have highlighted the role of alternative splicing (AS) in increasing transcriptome complexity. This role of AS, combined with the relation of aberrant splicing to malignant states, motivated two streams of research, experimental and computational. The first ...
Read More »Personal genome approach to RNA-Seq read alignment enables the discovery of splicing variations
RNA-seq is a powerful and popular technology for studying posttranscriptional regulation of gene expression, such as alternative splicing. The first step in analyzing RNA-seq data is to map the sequenced reads back to the genome. However, commonly used RNA-seq aligners ...
Read More »GFusion – an Effective Algorithm to Identify Fusion Genes from Cancer RNA-Seq Data
Fusion gene derived from genomic rearrangement plays a key role in cancer initiation. The discovery of novel gene fusions may be of significant importance in cancer diagnosis and treatment. Meanwhile, next generation sequencing technology provide a sensitive and efficient way ...
Read More »ASplice – a scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms
With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from high-throughput sequencing data, they are very memory-intensive, limiting their ...
Read More »Recent Publications Demonstrate Rapid Adoption of SMRT Sequencing for Plant and Animal Transcriptome Analysis
A series of recent peer-reviewed scientific publications highlights the growing use of Single Molecule, Real-Time (SMRT®) Sequencing to annotate plant and animal genomes. These reports from the genomics community show that PacBio sequencing consistently detects more genes, alternative splicing events, ...
Read More »CASH – a constructing comprehensive splice site method for detecting alternative splicing events
RNA-sequencing (RNA-seq) can generate millions of reads to provide clues for analyzing novel or abnormal alternative splicing (AS) events in cells. However, current methods for exploring AS events are still far from being satisfactory. Here, researchers from Zhejiang A & ...
Read More »Researchers identify first familially-inherited fusion gene based on RNA-seq data
SplicingCodes.com’s scientists, in collaboration with colleagues from USA and China, have identified the KANSARL fusion gene as the first familially-inherited cancer susceptible fusion gene specific to the population of European ancestry origin. The KANSARL fusion gene is also the cancer ...
Read More »Detecting Alternatively Spliced Transcript Isoforms from Single-Molecule Long-Read Sequences without a Reference Genome
Alternative splicing (AS) is a major source of transcript and proteome diversity, but examining AS in species without well-annotated reference genomes remains difficult. Research on both human and mouse has demonstrated the advantages of using Iso-Seq™ data for isoform-level transcriptome ...
Read More »Researchers identify genetic variants controlling alternative splicing of transcribed RNA in the human brain
from Science Daily – New research has identified sections of DNA associated with altered regulation of gene expression underlying schizophrenia. The implicated loci contribute to schizophrenia risk by affecting alternative splicing, part of the process that translates the same DNA ...
Read More »Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates
A key component in many RNA-Seq based studies is the production of multiple replicates for varying experimental conditions. Such replicates allow to capture underlying biological variability and control for experimental ones. However, during data production researchers often lack clear definitions ...
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