Researchers at the Broad Institute present "a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq" in a Genome Biology paper published online in advance. The Broad team says its approach produces highly reproducible expression profiles that enrich up to 40-fold for non-rRNA transcripts and correlate "well with profiles representing undepleted total RNA."
Brown University's Suzanne Sindi and her colleagues present GASVPro, "an algorithm combining both paired read and read depth signals into a probabilistic model which can analyze multiple alignments of reads," in a paper published online in advance in Genome Biology this week. Sindi et al. say that their algorithm "outperforms existing methods with a 50 percent to 90 percent improvement in specificity on deletions and a 50 percent improvement on inversions."
In another paper published online in advance this week, Indiana University's Kimberley Cook and her colleagues introduce a large-scale resource development project at the school's Bloomington Drosophila Stock Center, for which they are using an FLP-mediated recombination between FRT-bearing transposon insertion approach to generate chromosomal deletions. "Drosophila melanogaster now has the most extensive genomic deletion coverage and breakpoint subdivision as well as the most comprehensive inventory of haploinsufficient genes of any multicellular organism," the authors write. "The improved selection of chromosomal deletion strains will be useful to nearly all Drosophila researchers."