Data Analysis

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

rna-seq

High-throughput transcriptome sequencing (RNA-seq) technology promises to discover novel protein-coding and non-coding transcripts, particularly the identification of long non-coding RNAs (lncRNAs) from de novo sequencing data. This requires tools that are not restricted by prior gene annotations, genomic sequences and ...

Read More »

Seqnature – RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Population

rna-seq

Massively parallel RNA sequencing (RNA-seq) has yielded a wealth of new insights into transcriptional regulation. A first step in the analysis of RNA-seq data is the alignment of short sequence reads to a common reference genome or transcriptome. Genetic variants ...

Read More »

XSAnno – a framework for building ortholog models in cross-species transcriptome comparisons

rna-seq

The accurate characterization of RNA transcripts and expression levels across species is critical for understanding transcriptome evolution. As available RNA-seq data accumulate rapidly, there is a great demand for tools that build gene annotations for cross-species RNA-seq analysis. However, prevailing ...

Read More »

Genome-wide map of regulatory interactions in the human genome

rna-seq

Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. Researchers at Stanford University School of Medicine generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, ...

Read More »

RNA-Seq with iReport and InSilico DB

rna-seq

RNA-Seq, or transcriptome sequencing, continues to be an exciting way to explore gene expression using next-generation sequencing (NGS). But for many researchers, the interpretation of RNA-Seq data remains a daunting task because they are using spreadsheets to read transcript names ...

Read More »

GSAASeqSP: A Toolset for Gene Set Association Analysis of RNA-Seq Data

RNA-Seq is quickly becoming the preferred method for comprehensively characterizing whole transcriptome activity, and the analysis of count data from RNA-Seq requires new computational tools. A team led by researchers at Southwest University, China developed GSAASeqSP, a novel toolset for ...

Read More »

miRPlant – an integrated tool for identification of plant miRNA from RNA sequencing data

rna-seq

Small RNA sequencing is commonly used to identify novel miRNAs and to determine their expression levels in plants. There are several miRNA identification tools for animals such as miRDeep, miRDeep2 and miRDeep*. miRDeep-P was developed to identify plant miRNA using ...

Read More »

RNAcentral 1.0 provides a single access point to non-coding RNA data, vastly improving research into gene products

rna-seq

RNAcentral, the first unified resource for all types of non-coding RNA data, has been launched today by the RNAcentral Consortium. It aggregates information from a federation of expert databases, and provides tools for easy browsing. The initial release of RNAcentral ...

Read More »

subSeq – Determining appropriate sequencing depth through efficient read subsampling

rna-seq

Next-generation sequencing experiments, such as RNA-Seq, play an increasingly important role in biological research. One complication is that the power and accuracy of such experiments depends substantially on the number of reads sequenced, so it is important and challenging to ...

Read More »

SUPPA – a super-fast pipeline for alternative splicing analysis from RNA-Seq

rna-seq

High-throughput RNA sequencing allows genome-wide analyses of pre-mRNA splicing across multiple conditions. However, the increasing number of available datasets represents a major challenge in terms of time and storage required for analyses. Now, a team led by researchers at the ...

Read More »