JDotter specifications

Information


Unique identifier OMICS_15405
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 Yes

Versioning


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Documentation


Maintainer


  • person_outline CodonStatistics Team <>

Additional information


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JDotter article

JDotter citations

 (3)
2011
PMCID: 3218844

[…] lncrna-tare sequences based on the predicted lncrna-tare-4l sequence. we then retrieved fasta sequence of the most telomere-proximal 50,000 bp on each chromosome end from plasmodb v6.5, and used jdotter [83] software to create dna dotplots mapping the telomeric repeats, tares 1 through 5, rep20, and the first predicted gene on each end. we placed each predicted lncrna-tare gene onto […]

2007
PMCID: 1783846

[…] vocs initially groups orthologous genes into families based on blastp scores, these can be manually checked and altered if necessary., dotplots of fv3 and giv were done using jdotter [33]. jdotter provides an interactive input window that links jdotter to the vocs database. the sequences for the fv3 and giv were obtained through the vocs database., the author(s) declare […]

2005
PMCID: 1087509

[…] survey of all other poxviruses is needed in order to determine the extent of these possible gene acquisitions., dotplots for the molluscum contagiosum virus genome were created and visualized using jdotter with a default window size of 26 nucleotides using a minimum cut-off score of 40 and a maximum cut-off score of 100 on the greymap tool in order to better visualize the unique background […]

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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