Annotation

The recently introduced Kallisto pseudoaligner has radically simplified the quantification of transcripts in RNA-sequencing experiments.  Researchers from the Keck School of Medicine of USC offer cloud-scale RNAseq pipelines Arkas-Quantification, which deploys Kallisto for parallel cloud computations, and Arkas-Analysis, which annotates ...

Next generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotation of the extensive amounts of small non-coding ...

Researchers at the University of Würzburg have constructed a powerful and modular pipeline called ANNOgesic that provides the required analyses and simplifies RNA-Seq-based bacterial and archaeal genome annotation. It is a modular, command-line tool that can integrate different types of RNA-Seq data ...

In the last decade, advanced functional genomics approaches and deep sequencing have allowed large-scale mapping of histone modifications and other epigenetic marks, highlighting functional relationships between chromatin organization and genome function. Here, researchers from the Sapienza University of Rome propose ...

Long intergenic noncoding RNAs (lincRNAs) , which are larger than 200 nucleotides and transcribed from the intergenic regions of protein coding genes, have been shown by accumulating findings to be widely expressed and extensively functional in many cellular processes. Nevertheless, ...

High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, ...

Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering ~90% of the genome. In addition ...

Small non-coding RNAs, in particular microRNAs, are critical for normal physiology and are candidate biomarkers, regulators, and therapeutic targets for a wide variety of diseases. There is an ever-growing interest in the comprehensive and accurate annotation of microRNAs across diverse ...

The vast majority of human multiexon genes undergo alternative splicing and produce a variety of splice variant transcripts and proteins, which can perform different functions. These protein-coding splice variants (PCSVs) greatly increase the functional diversity of proteins. Most functional annotation ...

Grafting of cell lines and primary tumours is a crucial step in the drug development process between cell line studies and clinical trials. AstraZeneca researchers have developed disambiguate, a program for computationally separating the sequencing reads of two species derived ...