Tag Archives: genome

Enabling large-scale next-generation sequence assembly with Blacklight

rna-seq

A variety of extremely challenging biological sequence analyses were conducted on the XSEDE large shared memory resource Blacklight, using current bioinformatics tools and encompassing a wide range of scientific applications. These include genomic sequence assembly, very large metagenomic sequence assembly, ...

Read More »

RNA Sequencing Analysis Reveals HeLa Cell Contamination

rna-seq

Nasopharyngeal carcinoma (NPC) cell lines are important model systems for analyzing the complex life cycle and pathogenesis of Epstein-Barr virus (EBV). Using an RNA-seq-based approach, researchers from Tulane University Health Sciences Center found HeLa cell contamination in several NPC cell ...

Read More »

Transcriptome Sequencing reveals that species diversity is predictable

rna-seq

Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species. This pivotal concept of population genetics has implications for species health, domestication, management and conservation. Levels of genetic diversity seem to vary ...

Read More »

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 ...

Read More »

piClust: A density based piRNA clustering algorithm

rna-seq

Piwi-interacting RNAs (piRNAs) are recently discovered, endogenous small non-coding RNAs. piRNAs protect the genome from invasive transposable elements (TE) and sustain integrity of the genome in germ cell lineages. Small RNA-sequencing data can be used to detect piRNA activations in ...

Read More »