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JDotter specifications

Information


Unique identifier OMICS_15405
Name JDotter
Alternative name Java-Dotter
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Output data Dot plots
Output format JPEG or JDotter
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Requirements
JRE
Maintained No

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Publication for Java-Dotter

JDotter citations

 (12)
library_books

The End of a 60 year Riddle: Identification and Genomic Characterization of an Iridovirus, the Causative Agent of White Fat Cell Disease in Zooplankton

2018
PMCID: 5873915
PMID: 29487186
DOI: 10.1534/g3.117.300429

[…] and indels, respectively. The score cutoff was 40, and the maximum period size was 500 (). For visualization and annotation, the software tool Artemis was used (). Collinearity analyses were done by JDotter (). DNAPlotter was used to generate the DNA map (). […]

library_books

Ribosomal RNA Genes Contribute to the Formation of Pseudogenes and Junk DNA in the Human Genome

2017
Genome Biol Evol
PMCID: 5381670
PMID: 28204512
DOI: 10.1093/gbe/evw307

[…] had large segments of rDNA-like sequence. The alignment map provided in is modified from the graphical output produced during the BLAST alignment run (; ). Dot plots were produced using the program JDotter v1.0 (). […]

call_split

Characterization and Genomic Study of the Novel Bacteriophage HY01 Infecting Both Escherichia coli O157:H7 and Shigella flexneri: Potential as a Biocontrol Agent in Food

2016
PLoS One
PMCID: 5201272
PMID: 28036349
DOI: 10.1371/journal.pone.0168985
call_split See protocol

[…] nce alignments were conducted using MEGA6 [] and BLAST2SEQ programs []. The genome sequence was handled and edited using Artemis16 [], and comparative genome analysis was performed using ACT12 [] and JDotter []. […]

call_split

Complete Genome Analysis of a Rabbit Rotavirus Causing Gastroenteritis in a Human Infant

2015
Viruses
PMCID: 4353919
PMID: 25690801
DOI: 10.3390/v7020844
call_split See protocol

[…] 00 replicates) was performed to measure the reliability of the tree topologies. For the identification of rearrangements and further comparison between sequences, the bioinformatics tools GeneDoc and JDotter were used [,]. […]

library_books

Genomic Diversity in Two Related Plant Species with and without Sex Chromosomes Silene latifolia and S. vulgaris

2012
PLoS One
PMCID: 3290532
PMID: 22393373
DOI: 10.1371/journal.pone.0031898

[…] //www.giriinst.org/censor/index.php) and with Repeat Masker (http://www.repeatmasker.org). For full length retroelement identification we used LTR Finder (http://tlife.fudan.edu.cn/ltr_finder/) and JDotter (http://athena.bioc.uvic.ca/QuickStart/JDotter). The other simple sequence analyses were completed using The Sequence Manipulation Suite - version 2 (SMS2) (http://www.bioinformatics.org/sms […]

call_split

Mobile Regulatory Cassettes Mediate Modular Shuffling in T4 Type Phage Genomes

2010
Genome Biol Evol
PMCID: 2839356
PMID: 20333230
DOI: 10.1093/gbe/evq006
call_split See protocol

[…] 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 Center for Biotechnology Inf […]

Citations

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JDotter institution(s)
Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
JDotter funding source(s)
This work was supported by funds from NSERC OPG0155125-01 and NIH U01-AI48653-02.

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