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PhagesDB specifications

Information


Unique identifier OMICS_14948
Name PhagesDB
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Documentation


Maintainer


  • person_outline Graham Hatfull

Publication for PhagesDB

PhagesDB citations

 (32)
library_books

Genomic Sequence of Mycobacteriophage OKCentral2016

2018
Genome Announc
PMCID: 5824014
PMID: 29472341
DOI: 10.1128/genomeA.01208-17

[…] 155, and OKCentral2016 were similar, at 67.4% and 65.1%, respectively (). OKCentral2016 was shown to align most with two other A10 subcluster phages, Chupacabra and Goose, by using a BLASTn search on PhagesDB.org with an expected value of 0.0 and a minimum identity value of 99%. OKCentral2016 shared a strong syntenic region coding for lysin A, lysin B, terminase, portal, capsid maturation protease […]

library_books

Complete Genome Sequence of Cluster J Mycobacteriophage Superphikiman

2018
Genome Announc
PMCID: 5794948
PMID: 29437101
DOI: 10.1128/genomeA.01538-17

[…] an average coverage of 335×. The genome was then annotated using the following databases and software: DNA Master (http://cobamide2.bio.pitt.edu), Glimmer (), GeneMark (), Starterator, Phamerator (), PhagesDB.org, NCBI BLAST and Conserved Domain Database at NCBI (, ), HHPRED (), ARAGORN (), tRNAscan-SE (), and PECAAN (http://pecaan.kbrinsgd.org).Superphikiman is a member of actinobacteriophage clu […]

library_books

An inclusive Research Education Community (iREC): Impact of the SEA PHAGES program on research outcomes and student learning

2017
Proc Natl Acad Sci U S A
PMCID: 5754813
PMID: 29208718
DOI: 10.1073/pnas.1718188115

[…] , Science Education Alliance faculty teams contribute to quality control of both sequence data and genome annotation (). Two databases facilitate coordination of the scientific and programmatic data (phagesdb.org and https://seaphages.org, respectively).Because of the potential complexity of SEA-PHAGES, we used systems-level methods (, ) to construct a detailed pathway map ( and ) that relates pro […]

library_books

Complete Genome Sequence of Klebsiella pneumoniae Phages SopranoGao, MezzoGao, and AltoGao

2017
Genome Announc
PMCID: 5679790
PMID: 29122857
DOI: 10.1128/genomeA.01009-17

[…] . Therefore, regions upstream of the terminases were chosen as the canonical start sites for these genomes. All genes were predicted using Glimmer and GeneMarkS and corrected using DNA Master (http://phagesdb.org/DNAMaster/).Analysis of the SopranoGao, MezzoGao, and AltoGao genomes found 77, 77, and 53 open reading frames, respectively, and G+C contents of 57.26%, 50.97%, and 53.29%, respectively. […]

library_books

Complete Genome Sequences of Cluster A Mycobacteriophages BobSwaget, Fred313, KADY, Lokk, MyraDee, Stagni, and StepMih

2017
Genome Announc
PMCID: 5658500
PMID: 29074662
DOI: 10.1128/genomeA.01182-17

[…] notated using DNA Master (http://cobamide2.bio.pitt.edu), Glimmer (), GeneMark (), Starterator, Phamerator (), HHPRED (), BLASTp searches against the NCBI nonredundant and actinobacteriophage (http://phagesdb.org) databases (, ), Aragorn (), tRNAscanSE (), and PECAAN (http://pecaan.kbrinsgd.org). Phage features are listed in .All of the genomes are approximately 50 kb long and have nucleotide sequ […]

call_split

Broad range lytic bacteriophages that kill Staphylococcus aureus local field strains

2017
PLoS One
PMCID: 5526547
PMID: 28742812
DOI: 10.1371/journal.pone.0181671
call_split See protocol

[…] genomes sequences, resulting in an average of 999-fold coverage. The hypothetical open reading frames (ORF) present in the phage genomes were predicted by using GeneMark program [], DNAMaster (http://phagesdb.org/DNAMaster/) and RAST [] and were manually curated. Protein similarity was evaluated with BLASTP. Structural predictions and motif searches were done with Pfam and InterProScan [,]. ARNold […]

Citations

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PhagesDB institution(s)
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
PhagesDB funding source(s)
This work has been supported by the Howard Hughes Medical Institute [grant number 54308198]; and by the National Institutes of Health [grant numbers GM093901, GM116884].

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