Protocols

GraphDNA specifications

Information


Unique identifier OMICS_15410
Name GraphDNA
Alternative name DNA Skew Graphing
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data The input can consist of a single file containing one or more DNA sequences or a series of separate sequence files can be loaded.
Input format FASTA, EMBL, GENBANK
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License Other
Computer skills Medium
Stability Stable
Requirements
JRE
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Additional information


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Publication for DNA Skew Graphing

GraphDNA citations

 (2)
call_split

The Mitochondrial Genome of Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) Supports Intramolecular Recombination as the Primary Mechanism of Gene Rearrangement in Octocoral Mitochondrial Genomes

2012
Genome Biol Evol
PMCID: 3468961
PMID: 22975720
DOI: 10.1093/gbe/evs074
call_split See protocol

[…] nd determine the structure of tRNA genes; ribosomal RNA gene boundaries were determined based only on alignment similarities. Base composition was determined using LaserGene (EditSeq module), and the GraphDNA package () was used to analyze strand-specific compositional asymmetry (purine, keto, and GC-skew). To identify features associated with origins of replication, we used the DNA-Walk method of […]

library_books

ModuleOrganizer: detecting modules in families of transposable elements

2010
BMC Bioinformatics
PMCID: 2955051
PMID: 20860790
DOI: 10.1186/1471-2105-11-474

[…] get a global view of them. For Foldback4 sequences we needed to open 100 different alignments. In practice, studies with more than 5 sequences become tedious.GraphDNA http://athena.bioc.uvic.ca/tools/GraphDNA[] uses fixed parameters for the multiple alignment. GraphDNA provides many views of the alignment such as 'Purine Skew', 'AT Skew' and 'DNA Walker'. These views show the skew of nucleotide co […]

GraphDNA institution(s)
Department of Microbiology and Biochemistry, University of Victoria, Victoria, BC, Canada
GraphDNA funding source(s)
This work was funded by NIAID grant HHSN266200400036C and Canadian NSERC Strategic Grant STPGP 269665-03.

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