Tag Archives: genome annotation

Vast amounts of next generation sequencing RNA data has been deposited in archives, accompanying very diverse original studies. The data is readily...

High-throughput RNA sequencing has proven invaluable not only to explore gene expression, but also for both gene prediction and genome annotation. However, RNA sequencing, carried out on tens or even hundreds of samples, requires easy...

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, ...

Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction ...

Annotation of complex genomes has evolved significantly but many remain far from complete. Several published transcript assembly programmes were tested on RNA-sequencing (RNA-seq) data to determine their effectiveness in identifying novel genes to improve the rice genome annotation. The assembly ...

With the development of high-throughput sequencing techniques, more and more genomes were sequenced and assembled. However, annotating a genome’s structure rapidly and expressly remains challenging. Current eukaryotic genome annotations require various, abundant supporting data, such as: species-specific and cross-species protein ...

Analysis of differential gene expression by RNA sequencing (RNA-Seq) is frequently done using feature counts, i.e. the number of reads mapping to a gene. However, commonly used count algorithms (e.g. HTSeq) do not address the problem of reads aligning with ...

Insects are one of the largest classes of animals on Earth and constitute more than half of all living species. The i5k initiative has begun sequencing of more than 5,000 insect genomes, which should greatly help in exploring insect resource ...