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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 in pipelines

 (6)
2017
PMCID: 5219674
PMID: 28061879
DOI: 10.1186/s13071-016-1956-9

[…]  “invertebrate mito”, and cove score cut-off = 0.1, and the software arwen (http://130.235.46.10/arwen/) []. the map of the species was visualized using the genome vx online tool (http://wolfe.ucd.ie/genomevx/) []. repeat sequences were found using spectral repeat finder v1.1 []. strand asymmetry was calculated using the formulas: at skew = (a-t)/(a + t) and gc skew = (g-c)/(g + c) []. codon usage […]

2017
PMCID: 5551029
PMID: 28793854
DOI: 10.1186/s12864-017-3956-3

[…] except for a word size value of 60., plastomes were annotated using dogma [] and through comparison with the sequences of published early-diverging eudicot plastomes. physical maps were drawn using genomevx [], followed by subsequent manual editing with adobe illustrator cs5. boundaries for trnas were identified with trnascan-se 1.21 [] and confirmed by comparison with available early-diverging […]

2016
PMCID: 4938499
PMID: 27391235
DOI: 10.1371/journal.pone.0158488

[…] genome was annotated using the annotator dogma [], coupled with manual corrections. for all of the trna genes, the annotations were verified using trnascan-se1.21 []. the genome map was drawn by genomevx []., the complete cp genomes of s. dentata and five other lamiales species were compared using the mvista program []. the boundaries between ir and sc regions of these species were also […]

2015
PMCID: 4548089
PMID: 26379689
DOI: 10.3389/fpls.2015.00662

[…] (). to further verify the identified trna genes, the trnascan-se 1.21 program was used to predict their corresponding structures (). the genome map of m. yunnanensis and m. balansae was drawn by genomevx ()., after alignment using clustal x 1.83 (), the sequences were manually adjusted with bioedit software (http://www.mbio.ncsu.edu/bioedit/bioedit.html). further, we conducted a sliding […]

2014
PMCID: 4137670
PMID: 25165620
DOI: 10.7717/peerj.484

[…] usage profiles of pcgs were analyzed. the newly sequenced and assembled p. westermani mtdna was annotated using mitos and the output file was further used to sketch the newly sequenced genome with genomevx at http://wolfe.ucd.ie/genomevx/., dna sequences of the 12 protein-coding genes from 13 representative trematode, cestode and nematode species were retrieved (), aligned in clustal w […]


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GenomeVx in publications

 (46)
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] 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 […]

PMCID: 5807412
PMID: 29459880
DOI: 10.3389/fpls.2018.00099

[…] 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 […]

PMCID: 5732391
PMID: 29246263
DOI: 10.1186/s13104-017-3077-8

[…] 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 […]

PMCID: 5695614
PMID: 29095864
DOI: 10.1371/journal.pone.0187104

[…] for protein-coding sequences; trna scan-se [] for the trna sequences and rnammer [] for ribosomal rna sequences. all annotations were then manually checked. finalized genome maps were created with genomevx []., all available plastid genomes of the stramenopiles were downloaded from ncbi genbank (https://www.ncbi.nlm.nih.gov/genbank/, consulted on 17 may 2016). a list of annotated genes […]

PMCID: 5615360
PMID: 28902130
DOI: 10.3390/genes8090227

[…] genetic code. blastx and blastn searches were performed to accurately annotate the genes encoding proteins and the locations of trnas. the whole chloroplast genome map was generated using genomevx []., codon usage was determined for all protein-coding genes. to examine the deviation in synonymous codon usage, avoiding the influence of the amino acid composition, the relative […]


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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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