Phage Classification Tool Set statistics

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Protocols

Phage Classification Tool Set specifications

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Unique identifier OMICS_17801
Name Phage Classification Tool Set
Interface Web user interface
Restrictions to use None
Input data Proteins of your single phage to be classified. Files must contain amino acids.
Input format FASTA
Programming languages Perl
Computer skills Basic
Stability Stable
Source code URL http://www.phantome.org/PHACTS/PHACTS-0.3.tar.gz
Maintained No

Publication for Phage Classification Tool Set

Phage Classification Tool Set citations

 (6)
library_books

Characterizing Phage Genomes for Therapeutic Applications

2018
Viruses
PMCID: 5923482
PMID: 29642590
DOI: 10.3390/v10040188

[…] of deleterious genes is analyzed by computational methods. Likewise, phage lifestyle is analyzed first by experimental methods in the laboratory, then additionally evaluated by computational methods. Phage Classification Tool Set (PHACTS) [] is an example of a tool that can be used for computational analysis of lifestyle. Lifestyle of a phage can be classified by two different states, lytic or lys […]

call_split

Complete Nucleotide Sequence of Klebsiella pneumoniae Bacteriophage vB_KpnM_KpV477

2017
Genome Announc
PMCID: 5597747
PMID: 28912306
DOI: 10.1128/genomeA.00694-17
call_split See protocol

[…] epressors, and antirepressors, expressed during the prophage stage, were not identified in the KpV477 genome. These data, as well as the results of a one-step growth experiment and analysis using the Phage Classification Tool Set (), indicate that KpV477 is a lytic bacteriophage.The BLASTn () results showed that the phage KpV477 genome exhibits high similarity (94 to 96%) with Klebsiella phages JD […]

library_books

A widespread family of polymorphic toxins encoded by temperate phages

2017
BMC Biol
PMCID: 5576092
PMID: 28851366
DOI: 10.1186/s12915-017-0415-1

[…] respectively. The order, the family, the type of nucleic acid, and the bacterial host of bacteriophages were extracted from the GenBank files. The lifestyle of Caudovirales phages was predicted using Phage Classification Tool Set (PHACTS) v0.3 [] (as in []). PHACTS predicts the lifestyle of a phage (i.e., virulent or temperate) from genomic data using both a similarity and a supervised random fore […]

library_books

Distinct Biological Potential of Streptococcus gordonii and Streptococcus sanguinis Revealed by Comparative Genome Analysis

2017
Sci Rep
PMCID: 5462765
PMID: 28592797
DOI: 10.1038/s41598-017-02399-4

[…] nucleotide sequence identity cutoff values of 70% identity and 70% coverage. An intact prophage was defined by achieving scores ≥90 by PHAST. To predict the lifestyle of the prophage, we utilized the Phage Classification Tool Set (PHACTS) which involved a novel similarity algorithm and Random Forest Classifier. The file which contains the protein sequences of the predicted genes in the phage as up […]

call_split

A marine inducible prophage vB_CibM P1 isolated from the aerobic anoxygenic phototrophic bacterium Citromicrobium bathyomarinum JL354

2014
Sci Rep
PMCID: 4236739
PMID: 25406510
DOI: 10.1038/srep07118
call_split See protocol

[…] further analysis. The beginning and end of a specific prophage genome were estimated based on the annotations of surrounding genes. The complete prophage genome was used to predict lifestyle with the Phage Classification Tool Set (PHACTS) (http://www.phantome.org/PHACTS/).A tRNA search was performed in the prophage genome using tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE). Homologous prophage […]

library_books

Molecular Characterization of Podoviral Bacteriophages Virulent for Clostridium perfringens and Their Comparison with Members of the Picovirinae

2012
PLoS One
PMCID: 3362512
PMID: 22666499
DOI: 10.1371/journal.pone.0038283

[…] 1.softberry.com/berry.phtml; Mount Kisco, NY, USA) programs. Final genome sequences were also submitted to the IMG/ER pipeline for gene predictions and initial annotation . The computational approach Phage Classification Tool Set (PHACTS) was developed to classify phages as to whether the lifestyle of a phage, described by its proteome, is virulent or temperate by using the known phage genomes in […]


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Phage Classification Tool Set institution(s)
Computational Science Research Center, San Diego State University, San Diego, CA, USA; Department of Mathematics and Statistics, San Diego State University, San Diego, CA, USA; Department of Computer Science, San Diego State University, San Diego, CA, USA; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA

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