Tag Archives: isoforms

NMFP – a non-negative matrix factorization based preselection method to identify mRNA isoforms from RNA-seq data

rna-seq

The advent of next-generation RNA sequencing (RNA-seq) has greatly advanced transcriptomic studies, including system-wide identification and quantification of mRNA isoforms under various biological conditions. A number of computational methods have been developed to systematically identify mRNA isoforms in a high-throughput ...

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CLASS – Splice Variant Annotation from RNA-Seq Reads

rna-seq

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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Bitseq found to produce the most accurate measures of gene expression

rna-seq

RNA-sequencing data analysis method BitSeq developed by Academy Research Fellow Antti Honkela?s research group and University of Manchester researchers has been found to be the most accurate gene transcript expression estimation method in a large international assessment. The method is ...

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sQTLseekeR – Identification of genetic variants associated with alternative splicing

rna-seq

Identification of genetic variants affecting splicing in RNA sequencing population studies is still in its infancy. Splicing phenotype is more complex than gene expression and ought to be treated as a multivariate phenotype to be recapitulated completely. Here a team ...

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SAT-Assembler – A Scalable and Accurate Targeted Gene Assembly Tool for Next-Generation Sequencing Data

Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, ...

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