In Genome Biology this week, researchers in Australia present a scaling normalization method for the differential expression analysis of RNA-seq data. The authors write that, because RNA-seq is likely to become the choice platform for interrogating RNA, and because normalization is an essential step in the analysis, their method proves to be simple. It shows "dramatically improved results ... in simulated and publicly available data sets," they add.
Researchers in Singapore present their tool for comprehensive chromatin interaction analysis with paired-end tag sequencing, or ChIA-PET, in Genome Biology this week. The authors write that the ChIA-PET software can be used to study genome-wide long-range chromatin interactions bound by protein factors. The researchers report that their technology is "fast, accurate, comprehensive, user-friendly, and open source."
Yale University and Wellcome Trust Sanger Institute scientists report their identification and analysis of unitary pseudogenes in humans and other primates. The team writes that although unitary pseudogenes represent only a small portion of all annotated pseudogenes in the genome, they constitute distinct functional losses over time, shedding light on human and primate evolution. They found 11 unitary pseudogenes to be polymorphic, containing both fuctional and nonfunctional alleles in the human population.
European researchers this week present XGAP, a "software model for the genotype and phenotype community." The team writes that users can either download standard XGAP or generate a custom version using a tool with programming interfaces to R-software and web services. "Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans," the team writes.