GenomeVx

[…]  “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 […]

[…] 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 […]

[…] 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 […]

[…] (). 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]