PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies - Wikidata - awgldk - TriplyDB

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

http://www.wikidata.org/entity/Q36228443

about

Emerging methods to study bacteriophage infection at the single-cell level Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities Genomic and Functional Portrait of a Highly Virulent, CTX-M-15-Producing H30-Rx Subclone of Escherichia coli Sequence Type 131.SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data Silencing of cryptic prophages in Corynebacterium glutamicum MetaPhinder-Identifying Bacteriophage Sequences in Metagenomic Data Sets A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes.Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens.Orthologous gene clusters and taxon signature genes for viruses of prokaryotes Applying Shannon's information theory to bacterial and phage genomes and metagenomes Leptospiral pathogenomics.RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome.Prophage-like elements present in Mycobacterium genomes Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.VirSorter: mining viral signal from microbial genomic data Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum Living in an Extremely Polluted Environment: Clues from the Genome of Melanin-Producing Aeromonas salmonicida subsp. pectinolytica 34melT.A novel chimeric prophage vB_LdeS-phiJB from commercial Lactobacillus delbrueckii subsp. bulgaricus.Whole-Genome Sequencing Allows for Improved Identification of Persistent Listeria monocytogenes in Food-Associated Environments Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton Genomic analysis of a nontoxigenic, invasive Corynebacterium diphtheriae strain from Brazil.PHASTER: a better, faster version of the PHAST phage search tool Factors behind junk DNA in bacteria Comparative Genomics Analysis of Two Different Virulent Bovine Pasteurella multocida Isolates.Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences.Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay PhagePhisher: a pipeline for the discovery of covert viral sequences in complex genomic datasets.Explaining microbial phenotypes on a genomic scale: GWAS for microbes.Bacteriophages of leuconostoc, oenococcus, and weissella.Computational approaches to predict bacteriophage-host relationships.VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics Lysogeny in nature: mechanisms, impact and ecology of temperate phages.A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements HostPhinder: A Phage Host Prediction Tool.Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction.

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PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

http://www.wikidata.org/entity/Q36228443

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Sajia Akhter

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Insights on Evolution of Virulence and Resistance from the Complete Genome Analysis of an Early Methicillin-Resistant Staphylococcus aureus Strain and a Biofilm-Producing Methicillin-Resistant Staphylococcus epidermidis Strain

The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice

Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species

The complete genome sequence of Mycobacterium bovis

Complete genome sequence of an M1 strain of Streptococcus pyogenes

Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance

The complete genome sequence of Mycobacterium avium subspecies paratuberculosis

Genome sequence of enterohaemorrhagic Escherichia coli O157:H7

Analyzing genomes with cumulative skew diagrams

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e126

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