New developments in RiPP discovery, enzymology and engineering
Covering: up to June 2020 Ribosomally-synthesized and post-translationally modified
peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 …
peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 …
Current challenges and best-practice protocols for microbiome analysis
Analyzing the microbiome of diverse species and environments using next-generation
sequencing techniques has significantly enhanced our understanding on metabolic …
sequencing techniques has significantly enhanced our understanding on metabolic …
PHASTEST: faster than PHASTER, better than PHAST
Abstract PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is the
successor to the PHAST and PHASTER prophage finding web servers. PHASTEST is …
successor to the PHAST and PHASTER prophage finding web servers. PHASTEST is …
Polyvinyl chloride degradation by a bacterium isolated from the gut of insect larvae
Evidence for microbial degradation of polyvinyl chloride (PVC) has previously been
reported, but little is known about the degrading strains and enzymes. Here, we isolate a …
reported, but little is known about the degrading strains and enzymes. Here, we isolate a …
Producing polished prokaryotic pangenomes with the Panaroo pipeline
Population-level comparisons of prokaryotic genomes must take into account the substantial
differences in gene content resulting from horizontal gene transfer, gene duplication and …
differences in gene content resulting from horizontal gene transfer, gene duplication and …
VFDB 2019: a comparative pathogenomic platform with an interactive web interface
The virulence factor database (VFDB, http://www. mgc. ac. cn/VFs/) is devoted to providing
the scientific community with a comprehensive warehouse and online platform for …
the scientific community with a comprehensive warehouse and online platform for …
BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins
Interest in secondary metabolites such as RiPPs (ribosomally synthesized and
posttranslationally modified peptides) is increasing worldwide. To facilitate the research in …
posttranslationally modified peptides) is increasing worldwide. To facilitate the research in …
[HTML][HTML] A key genetic factor governing arabinan utilization in the gut microbiome alleviates constipation
Impaired gastrointestinal motility is associated with gut dysbiosis. Probiotics, such as
Bifidobacteria, can improve this bowel disorder; however, efficacy is strain-dependent. We …
Bifidobacteria, can improve this bowel disorder; however, efficacy is strain-dependent. We …
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
Background Identifying viral sequences in mixed metagenomes containing both viral and
host contigs is a critical first step in analyzing the viral component of samples. Current tools …
host contigs is a critical first step in analyzing the viral component of samples. Current tools …
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
Abstract The RAST (Rapid Annotation using Subsystem Technology) annotation engine was
built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard …
built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard …