Genome Biology – lots of exciting software this month

The August issue of Genome Biology is now available on our website, and it’s a bumper issue this month. As well as several high-quality research articles (such as the wallaby genome sequence, the transcriptome of regenerating heads in planarians and a comprehensive screen for substrates of the Chk1 checkpoint kinase), we have a number of exciting computational methods for analyzing high throughput genomics data.

Kim and Salzberg present TopHat-Fusion, a modified version of the popular TopHat package for analyzing RNA-seq datasets, that can identify transcripts from fusion genes. As fusion genes are often important in carcinogenesis (such as the canonical BCR-Abl fusion from the Philadelphia chromosome in some leukemias), this has important medical applications.

Uwe Ohler and colleagues present PARalyzer, a package for analyzing PAR-CLIP data. PAR-CLIP is a relatively new method for identifying where specific proteins bind to RNA molecules. PAR-CLIP stands for ‘Photoactivatable Ribonucleoside-enhanced Cross-Linking and Immuno-Precipitation’. Crosslinks are induced between proteins and RNA, and specific proteins pulled down using antibodies. The RNA fragments attached to the proteins can be determined using high throughput sequencing. Until now, packages for analyzing these data have been few, but the new method from Ohler’s group will help researchers interpret their results.

Shirley Liu and colleagues give us CISTROME, in which they have integrated 29 different packages to provide a complete suite for the analysis of ChIP-chip and ChIP-seq data at all stages, from preliminary peak calling, to downstream genome feature association, gene expression analyses and motif discovery. These have all been combined into an easy-to-use application based on the Galaxy open source framework.

After Jason Lieb’s ZINBA program that we published last month this goes to show that Genome Biology’s support for first-rate data analysis applications goes from strength to strength.

Andrew Cosgrove

Andrew obtained his PhD in molecular biology from the University of Dundee in 2005. He joined Genome Biology in 2009 after a post doctoral research position at the University of Sheffield investigating chromosome positioning during meiosis in yeast.
Andrew Cosgrove

View the latest posts on the On Biology homepage