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Protocols

GenomeVx specifications

Information


Unique identifier OMICS_15547
Name GenomeVx
Interface Web user interface
Restrictions to use None
Programming languages C, C++
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Gavin Conant

Publication for GenomeVx

GenomeVx citations

 (69)
library_books

Comparative genomics of the wheat fungal pathogen Pyrenophora tritici repentis reveals chromosomal variations and genome plasticity

2018
BMC Genomics
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] ndrial genomes were made using Mitos webserver [] and refined based on blast versus http://mitofun.biol.uoa.gr/ protein sequences. Circular visualisation of mitochondrial features was generated using GenomeVx web application (March 2016) []. The dothideomyceta mitochondrial apt8 and apt9 Mycosphaerella graminicola genes were retrieved from Genbank NC_010222.1:c34402-34256 and NC_010222.1:c23405-23 […]

call_split

Molecular Phylogeny and Dating of Forsythieae (Oleaceae) Provide Insight into the Miocene History of Eurasian Temperate Shrubs

2018
Front Plant Sci
PMCID: 5807412
PMID: 29459880
DOI: 10.3389/fpls.2018.00099
call_split See protocol

[…] gs. The cp genomes were annotated with DOGMA () to identify coding sequences and rRNAs. The tRNA sequences were also confirmed by tRNAscan-SE (). Genome maps were constructed using the Web-based tool GenomeVx (). Visualization of the alignment of chloroplast sequences was conducted with mVISTA, in which O. europaea was used as a reference sequence. Repetitive sequences were identified using REPute […]

library_books

Chloroplast genomes of Byrsonima species (Malpighiaceae): comparative analysis and screening of high divergence sequences

2018
Sci Rep
PMCID: 5797077
PMID: 29396532
DOI: 10.1038/s41598-018-20189-4

[…] ge_Analysis).Automatic annotation of B. coccolobifolia and B. crassifolia chloroplast genomes were generated by CpGAVAS and a circular representation of both sequences was drawn using the online tool GenomeVX. The draft annotations given by CpGAVAS were then manually corrected using the Artemis software and other plastid genomes for comparison. The complete chloroplast genomes of B. coccolobifolia […]

library_books

Method for the Identification of Taxon Specific k mers from Chloroplast Genome: A Case Study on Tomato Plant (Solanum lycopersicum)

2018
Front Plant Sci
PMCID: 5776150
PMID: 29387080
DOI: 10.3389/fpls.2018.00006

[…] n-specific k-mers in the chloroplast genome were found using the S. lycopersicum chloroplast sequence NC_007898.3 using Python scripts. A physical map of the tomato plant plastome was drawn using the GenomeVX software (). […]

library_books

The complete chloroplast genome sequence of Asian Palmyra palm (Borassus flabellifer)

2017
BMC Res Notes
PMCID: 5732391
PMID: 29246263
DOI: 10.1186/s13104-017-3077-8

[…] epth coverage, and eight contigs covering 92% of the entire cp genome was obtained. Specific PCR amplification and sequencing were performed to fill the missing gaps. The genome map was then drawn by GenomeVx [].The circular double-stranded DNA of the complete B. flabellifer cp genome is 160,021 bp in length (Fig. , GenBank Accession Number: KP_901247). It has a typical quadripartite structure com […]

library_books

The Complete Mitogenome of the Wood Feeding Cockroach Cryptocercus meridianus (Blattodea: Cryptocercidae) and Its Phylogenetic Relationship among Cockroach Families

2017
Int J Mol Sci
PMCID: 5713365
PMID: 29137151
DOI: 10.3390/ijms18112397

[…] , with an asymmetric nucleotide composition (45.20% A, 16.06% C, 9.74% G, and 29.00% T) and an AT bias (74.2%) (). The circular map of the C. meridianus mitogenome is shown in , drawn by the software GenomeVx []. AT content of the C. meridianus mitogenome (74.2%) is slightly higher than that of C. relictus (73.5%) and slightly lower than in C. kyebangensis (74.4%). Similar to other insects, it is […]

Citations

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GenomeVx institution(s)
Smurfit Institute of Genetics, Trinity College, University of Dublin, Dublin, Ireland
GenomeVx funding source(s)
This work was supported by Science Foundation Ireland.

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