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This Week in Nucleic Acids Research: Jan 18, 2017

Researchers from the Netherlands report on efforts to quickly detect gut microbial community contributors to antibiotic resistance in human pathogens with the Oxford Nanopore Technologies MinION nanopore sequencer. With a functional metagenomic and nanopore sequencing workflow dubbed poreFUME, the team mapped these gut resistomes in fecal samples collected over time from a patient treated with multiple antibiotics in the intensive care unit of a hospital in Utrecht. Based on findings from that analysis, the authors argue that poreFUME "provides a promising approach for efficient resistome profiling that could inform antibiotic treatment decisions in the future."

An international team led by investigators in France describes an alignment-free program for annotating long non-coding RNAs (lncRNAs) in whole transcriptome datasets. The approach — called "Flexible extraction of lncRNAs," or FEELnc — is designed to filter out non-lncRNA transcripts, evaluate possible lncRNAs, and classify verified lncRNAs, the researchers say. After assessing FEELnc performance for annotating Gencode and Noncode datasets, alongside five existing tools, they applied the method to RNA sequencing sets for 20 dog samples, uncovering almost 10,400 new lncRNAs and tens of thousands of messenger RNA transcripts.

By tapping available data for tens of thousands of transcription start sites in Arabidopsis thaliana and the Oryza sativa japonica rice plant, researchers from Saudi Arabia, Azerbaijan, and the US came up with the TSSPlant tool for predicting RNA polymerase II promoter sites in plants based on 18 sequence features. The TSSPlant computational tool "compares favorably with other known and available promoter predictors," the team writes, "and was applied for genome-wide analysis of promoter sequences in seven plant genomes."