Phage Classification Tool Set protocols

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Phage Classification Tool Set specifications

Information


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 in pipeline

2014
PMCID: 4236739
PMID: 25406510
DOI: 10.1038/srep07118

[…] 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 […]


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Phage Classification Tool Set in publications

 (5)
PMCID: 5923482
PMID: 29642590
DOI: 10.3390/v10040188

[…] 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 […]

PMCID: 5597747
PMID: 28912306
DOI: 10.1128/genomeA.00694-17

[…] 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 […]

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

[…] 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 […]

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

[…] in streptococcal c1 bacteriophage. this enzyme hydrolyzes the n-acetylmuramoyl-l-alanine amide bond between the glycan strand and the cross-linking peptide of peptidoglycan. we then utilized the phage classification tool set (phacts), which is an online computational tool, to classify the lifestyle of the mb451_1 prophage. phacts predicted the prophage mb451_1 to have a temperate lifestyle […]

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

[…] 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 […]


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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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