Magnus Representation of Genome Sequences.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of theoretical biology"
DOI: 10.1016/j.jtbi.2019.08.004
Abstract: We introduce an alignment-free method, the Magnus Representation, to analyze genome sequences. The Magnus Representation captures higher-order information in genome sequences. We combine our approach with the idea of k-mers to define an effectively computable… read more here.
Keywords: genome sequences; representation genome; magnus representation; bacterial genomes ... See more keywords
Complete, closed bacterial genomes from microbiomes using nanopore sequencing
Sign Up to like & getrecommendations! Published in 2020 at "Nature Biotechnology"
DOI: 10.1038/s41587-020-0422-6
Abstract: Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic positions of repeats is crucial for understanding the effect… read more here.
Keywords: microbiomes using; closed bacterial; bacterial genomes; nanopore sequencing ... See more keywords
Screening and characterization of prophages in Desulfovibrio genomes
Sign Up to like & getrecommendations! Published in 2018 at "Scientific Reports"
DOI: 10.1038/s41598-018-27423-z
Abstract: Bacteria of the genus Desulfovibrio belong to the group of Sulphate Reducing Bacteria (SRB). SRB generate significant liabilities in the petroleum industry, mainly due to their ability to microbiologically induce corrosion, biofilm formation and H2S… read more here.
Keywords: desulfovibrio genomes; screening characterization; complete prophages; bacterial genomes ... See more keywords
Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes.
Sign Up to like & getrecommendations! Published in 2021 at "RNA biology"
DOI: 10.1080/15476286.2021.1917891
Abstract: Comparative sequence analysis methods are highly effective for uncovering novel classes of structured noncoding RNAs (ncRNAs) from bacterial genomic DNA sequence datasets. Previously, we developed a computational pipeline to more comprehensively identify structured ncRNA representatives… read more here.
Keywords: structured ncrna; structured noncoding; bacterial genomes; novel structured ... See more keywords
Replication-Dependent Organization Constrains Positioning of Long DNA Repeats in Bacterial Genomes
Sign Up to like & getrecommendations! Published in 2022 at "Genome Biology and Evolution"
DOI: 10.1093/gbe/evac102
Abstract: Bacterial genome organisation is primarily driven by chromosome replication from a single origin of replication. However chromosomal rearrangements, which can disrupt such organisation, are inevitable in nature. Long DNA repeats are major players mediating rearrangements,… read more here.
Keywords: dna; dna repeats; replication; bacterial genomes ... See more keywords
Proksee: in-depth characterization and visualization of bacterial genomes.
Sign Up to like & getrecommendations! Published in 2023 at "Nucleic acids research"
DOI: 10.1093/nar/gkad326
Abstract: Proksee (https://proksee.ca) provides users with a powerful, easy-to-use, and feature-rich system for assembling, annotating, analysing, and visualizing bacterial genomes. Proksee accepts Illumina sequence reads as compressed FASTQ files or pre-assembled contigs in raw, FASTA, or… read more here.
Keywords: map; genomes proksee; bacterial genomes; proksee depth ... See more keywords
PHASTEST: faster than PHASTER, better than PHAST.
Sign Up to like & getrecommendations! Published in 2023 at "Nucleic acids research"
DOI: 10.1093/nar/gkad382
Abstract: PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is the successor to the PHAST and PHASTER prophage finding web servers. PHASTEST is designed to support the rapid identification, annotation and visualization of prophage sequences within… read more here.
Keywords: phast; visualization; prophage; phaster ... See more keywords
Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction
Sign Up to like & getrecommendations! Published in 2022 at "Microbial Genomics"
DOI: 10.1101/2022.04.29.490057
Abstract: Complete, accurate, cost-effective, and high-throughput reconstruction of bacterial genomes for large-scale genomic epidemiological studies is currently only possible with hybrid assembly, combining long- (typically using nanopore sequencing) and short-read (Illumina) datasets. Being able to utilise… read more here.
Keywords: cost; bacterial genomes; r10 kit12; reconstruction ... See more keywords
Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples
Sign Up to like & getrecommendations! Published in 2022 at "mSystems"
DOI: 10.1128/msystems.00491-22
Abstract: Obtaining complete and accurate genomes is crucial to the study of any organism. Previously, obtaining complete genomes of bacteria, including those of the human microbiome, frequently required isolation of the organism, as well as low-throughput,… read more here.
Keywords: obtaining complete; complete genomes; obtain complete; bacterial genomes ... See more keywords
Evolutionary Responses to Acquiring a Multidrug Resistance Plasmid Are Dominated by Metabolic Functions across Diverse Escherichia coli Lineages
Sign Up to like & getrecommendations! Published in 2022 at "mSystems"
DOI: 10.1128/msystems.00713-22
Abstract: Plasmids drive the spread of antimicrobial resistance genes between bacterial genomes. However, the evolutionary processes allowing plasmids to be assimilated by diverse bacterial genomes are poorly understood, especially in clinical pathogens. ABSTRACT Multidrug resistance (MDR)… read more here.
Keywords: metabolic functions; multidrug resistance; plasmid; bacterial genomes ... See more keywords
Assembly of 97 Novel Bacterial Genomes in the Microbial Community Affiliated with Polyvinyl Alcohol in Soil of Northern China
Sign Up to like & getrecommendations! Published in 2022 at "BioMed Research International"
DOI: 10.1155/2022/2229147
Abstract: Background Undeveloped ecosystems belong to rich source of microbial population, of which resources remain unearthed. A kind of polymeric compound system with high polyvinyl alcohol (PVA) content has been reported and named Taisui. Marker gene… read more here.
Keywords: novel bacterial; bacterial genomes; pva; polyvinyl alcohol ... See more keywords