Skip to main content
Premium Trial:

Request an Annual Quote

This Week in Nucleic Acids Research: Jul 8, 2015

Researchers at the University of Toronto and the Ontario Institute for Cancer Research introduce a software package called RNASequel that's designed to correct common alignment artifacts in RNA sequence alignments based on de novo splice junction patterns and fragment size distribution estimates when run alongside alignment algorithms. In their proof-of-principle study, the authors showed that this approach compared favorably with annotations done using STAR or Tophat2, improving alignments based on simulated datasets and providing a look at RNA editing sites in authentic RNA sequence data.

A team led by investigators at the Department of Energy's Joint Genome Institute introduces a strategy for defining microbial species and determining relationships between microbes based on their whole-genome sequences. By integrating information on genome-wide average nucleotide identity, or gANI, with alignment fractions between genomes, the researchers showed that it was possible to come up with more than 3,000 microbial species assignments reflecting 13,151 genome sequences that together made up tens of millions of genome pairs. "We propose that this … MiSI (microbial species Identifier) method be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment."

University of Maryland researchers tracked gene expression and transcript processing patterns in the intracellular protozoan parasite Leishmania major as it progresses from a non-infectious stage into a form that produces leishmaniasis symptoms. Based on the RNA sequence data generated for six L. major replicates over time, the team identified differential gene expression profiles and other transcriptional signatures associated with differentiation into the infectious state. As such, the study's author say, the data "provide a substantially more detailed interpretation of L. major biology that will inform the field and potentially provide additional data for drug discovery and vaccine development efforts."