ArticleBMC genomics2017
Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- Genome annotation ofMicrobiology resource announcements · 2026Article
- Isolation and characterization of TayeBlu, a novel bacteriophage ofMicrobiology spectrum · 2026Article
- Isolation and Genome Annotation of TicTac, an EK1 Cluster Bacteriophage with Podovirus Morphology.microPublication biology · 2026Article
- Isolation and genome annotation of Rowlf, a novel cluster EG bacteriophage with a purple acid phosphatase-like gene.Microbiology resource announcements · 2025Article
- Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle.bioRxiv : the preprint server for biology · 2024Article
- A synthetic biology approach to assemble and reboot clinically relevantMicrobiology spectrum · 2024Article
- Isolation and genome sequence annotation of SallyK, a newly discovered cluster EG bacteriophage infectingMicrobiology resource announcements · 2023Article
- Isolation and genome sequence annotation of KillerTomato, a newly discovered cluster EE bacteriophage infectingMicrobiology resource announcements · 2023Article
- Circular RNAs: New layer of complexity evading breast cancer heterogeneity.Non-coding RNA research · 2023Article
- Evidence of a Set of Core-Function Genes in 16 Bacillus Podoviral Genomes with Considerable Genomic Diversity.Viruses · 2023Article
- Phage Annotation Guide: Guidelines for Assembly and High-Quality Annotation.PHAGE (New Rochelle, N.Y.) · 2021Article
- CheckV assesses the quality and completeness of metagenome-assembled viral genomes.Nature biotechnology · 2021Article
- Isolation and Characterization ofMicroorganisms · 2020Article
- Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses.Journal of virological methods · 2020Article
- Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut.Microbiome · 2019Article
- Genomic Analysis of the Recent Viral Isolate vB_BthP-Goe4 Reveals Increased Diversity of φ29-Like Phages.Viruses · 2018Article
- Isolation of A NovelViruses · 2018Article
- PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data.Scientific reports · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
backgroundMost tailed bacteriophages (phages) feature linear dsDNA genomes. Characterizing novel phages requires an understanding of complete genome sequences, including the definition of genome physical ends.
resultWe sequenced 48 Bacillus cereus phage isolates and analyzed Next-generation sequencing (NGS) data to resolve the genome configuration of these novel phages. Most assembled contigs featured reads that mapped to both contig ends and formed circularized contigs. Independent assemblies of 31 nearly identical I48-like Bacillus phage isolates allowed us to observe that the assembly programs tended to produce random cleavage on circularized contigs. However, currently available assemblers were not capable of reporting the underlying phage genome configuration from sequence data. To identify the genome configuration of sequenced phage in silico, a terminus prediction method was developed by means of 'neighboring coverage ratios' and 'read edge frequencies' from read alignment files. Termini were confirmed by primer walking and supported by phylogenetic inference of large DNA terminase protein sequences.
conclusionsThe Terminus package using phage NGS data along with the contig circularity could efficiently identify the proximal positions of phage genome terminus. Complete phage genome sequences allow a proposed characterization of the potential packaging mechanisms and more precise genome annotation.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.