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JFreq specifications


Unique identifier OMICS_15532
Name JFreq
Alternative name Java Word Frequencies
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Stability Stable
Maintained No


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JFreq citations


Composite Conserved Promoter–Terminator Motifs (PeSLs) that Mediate Modular Shuffling in the Diverse T4 Like Myoviruses

Genome Biol Evol
PMCID: 4122927
PMID: 24951563
DOI: 10.1093/gbe/evu129
call_split See protocol

[…] ccessed June 22, 2014; heuristic approach for prokaryotes and viruses; >90 nt) for ORF determinations; 2) tRNA search using tRNAscan-SE (lowelab.ucsc.edu/tRNAscan-SE, last accessed June 22, 2014); 3) Java Word Frequencies (athena.bioc.uvic.ca/virology-ca-tools/jfreq/, last accessed June 22, 2014) and Dot Plot Alignments (MIPS Gepard; www.helmholtz-muenchen.de/icb/gepard, last accessed June 22, 201 […]


Phage Morphology Recapitulates Phylogeny: The Comparative Genomics of a New Group of Myoviruses

PLoS One
PMCID: 3391216
PMID: 22792219
DOI: 10.1371/journal.pone.0040102
call_split See protocol

[…] netic code) and GeneMark (exon.gatech.edu/GeneMark; heuristic approach for prokaryotes and viruses; >90 nt) for ORF determinations; 2) tRNA search using tRNAscan-SE (lowelab.ucsc.edu/tRNAscan-SE); 3) Java Word Frequencies (athena.bioc.uvic.ca) and Dot-Plot Alignments (MIPS Gepard; www.helmholtz-muenchen.de/en/mips/services/analysis-tools/gepard/index.html) for the exploration of DNA and protein “w […]


Mobile Regulatory Cassettes Mediate Modular Shuffling in T4 Type Phage Genomes

Genome Biol Evol
PMCID: 2839356
PMID: 20333230
DOI: 10.1093/gbe/evq006
call_split See protocol

[…] the T4-type phage server at Tulane University (http://phage.bioc.tulane.edu); 3) GLIMMER () and GeneMark () for open reading frame (ORF) determination; and 4) Java Word Frequencies and Java Dotter (http://athena.bioc.uvic.ca/tools/) for the exploration of DNA “words”/patterns; and 5) the Blast tools at National Ce […]


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JFreq institution(s)
Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada

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