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Protocols

Phamerator specifications

Information


Unique identifier OMICS_22327
Name Phamerator
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Database management system MySQL
Computer skills Medium
Requirements
pyro, clustalw, python-biopython, mysql-server, python-mysqldb, python-pygoocanvas, curl
Maintained No

Versioning


No version available

Maintainer


This tool is not maintained anymore.

Publication for Phamerator

Phamerator citations

 (62)
library_books

Genome Sequences of Ilzat and Eleri, Two Phages Isolated Using Microbacterium foliorum NRRL B 24224

2018
Genome Announc
PMCID: 5897797
PMID: 29650566
DOI: 10.1128/genomeA.00144-18

[…] that of the isolation host (68.7%; GenBank accession no. JYIU00000000).The genomes were annotated using DNA Master (http://cobamide2.bio.pitt.edu/), Glimmer (), GeneMark (), BLASTP (), HHpred (), and Phamerator (). A total of 62 and 63 protein-coding genes were identified in Ilzat and Eleri, respectively. The two phages share similar genome architectures and synteny, with DNA packaging, virion str […]

call_split

Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

2018
BMC Microbiol
PMCID: 5831693
PMID: 29490612
DOI: 10.1186/s12866-018-1159-y
call_split See protocol

[…] were analyzed and annotated using the genome editor DNAMaster (http://cobamide2.bio.pitt.edu). GenBank accession numbers are listed in Table . Genome comparisons were performed and represented using Phamerator and the database ‘Actinobacteriophage_685’ []. […]

library_books

Genomic Sequence of Mycobacteriophage OKCentral2016

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

[…] n-coding regions of the genome were detected using Glimmer () and GeneMark (). Starterator (https://seaphages.org/software/) was used to evaluate gene start codons. Gene function was determined using Phamerator () and BLASTn/BLASTp on PhagesDB.org. ARAGORN () and tRNAscan-SE () were used to analyze tRNA sequences within the genome. OKCentral2016 was shown to possess 84 protein-coding genes and 1 t […]

library_books

Complete Genome Sequence of Cluster J Mycobacteriophage Superphikiman

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

[…] efense systems. Other cluster J bacteriophages such as Courthouse have short reverse genes in this position; however, the number of genes present and the nucleotide sequences vary across this region (Phamerator.org). The immunity repressor in Superphikiman (gp191) is identical to the immunity repressor genes found in the cluster A1 bacteriophages Dynamix (gp75) (GenBank accession number AMD43071) […]

library_books

Genome Sequence of a Newly Isolated F2 Subcluster Mycobacteriophage from the Black Belt Geological Region of Western Alabama

2018
Genome Announc
PMCID: 5786693
PMID: 29371367
DOI: 10.1128/genomeA.01555-17

[…] the F2 subcluster is 56,236 bp, and the average gene number is 111. Demsculpinboyz and other F2 phages show high nucleotide similarity and share a conserved region in the first third of the genome. A Phamerator map of Che9d and Demsculpinboyz shows a decrease in nucleotide similarity at 30,000 bp ().Within the F2 subcluster, the Lysin A gene (Demsculpinboyz gp35) is represented by three variations […]

library_books

The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile

2018
Front Microbiol
PMCID: 5786514
PMID: 29403466
DOI: 10.3389/fmicb.2018.00026

[…] confirmed this finding, as only a low fraction of the genes was conserved in the phiCD5763-like phages (15%, 55/364), the phiCD2955-like phages (20%, 66/338), or all 10 big phage genomes (3%, 15/538).Phamerator defined 328 phams from the 10 big phage genome assemblies (Supplementary Material ). Sixty-six of these phams were omnipresent among phiCD5763-like and phiCD2955-like phage genomes (20%), b […]

Citations

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Phamerator institution(s)
Department of Biology, James Madison University, Harrisonburg, VA, USA; Pittsburgh Bacteriophage Institute and Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
Phamerator funding source(s)
Supported in part by a grant to the University of Pittsburgh by the Howard Hughes Medical Institute (HHMI) under HHMI’s Professors program; and by grants from NIH (GM51975), (GM093901) and (AI082527).

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