mVISTA protocols

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mVISTA specifications

Information


Unique identifier OMICS_26805
Name mVISTA
Interface Web user interface
Restrictions to use None
Input format FASTA
Programming languages Java
Computer skills Basic
Maintained Yes

Maintainer


  • person_outline In Dubchak <>

Publications for mVISTA

mVISTA in pipelines

 (24)
2018
PMCID: 5852582
PMID: 29438341
DOI: 10.3390/genes9020086

[…] checked for consistency. , multiple sequence alignments were processed with clustalx [] and manually edited to be optimized. genomic comparisons of cross-species were carried out by an online tool mvista []. , total rnas from pig, mouse, rat, chicken, and frog heart samples were isolated with trizol (invitrogen, carlsbad, ca, usa) and further treated with rq1 rnase-free dnase (promega, […]

2018
PMCID: 5854438
PMID: 29543905
DOI: 10.1371/journal.pone.0194613

[…] seven cp genomes were deposited in genbank (accession number mg200070, mg211818-mg211823)., a comparative plot consisting of full alignments of the cp genomes with annotations was produced by mvista using f. cirrhosa as the reference. the sequences were aligned using mega 6 [] and then manually adjusted using bioedit software (http://www.mbio.ncsu.edu/bioedit/bioedit.html). subsequently, […]

2017
PMCID: 5485006
PMID: 28261921
DOI: 10.1111/mec.14084

[…] supporting information). primers were designed manually or using the program primer3 (rozen & skaletsky ). to follow the structural evolution of the flc orthologues, sequences were aligned by mvista (mayor et al. ; frazer et al. ) and compared to a. thaliana flc. alignments were adjusted manually. exons (by using cdna data) and sequences with homology to known regulatory elements from flc […]

2017
PMCID: 5581188
PMID: 28863163
DOI: 10.1371/journal.pone.0184257

[…] maximum likelihood analysis was performed using mega6 with 1,000 bootstrap replicates []., highly divergent regions between eight aconitum species were confirmed based on mvista similarities, and primers were designed using primer-blast (ncbi). to amplify divergent regions, about 20 ng genomic dna was added to 20 ul pcr mixture (solg™ 2× taq pcr smart mix 1, solgent, […]

2017
PMCID: 5595811
PMID: 28900227
DOI: 10.1038/s41598-017-11206-z

[…] version 4.6 was applied to perform a cluster sequence analysis to check sequence identity between lncrnas and ests with a cutoff equal to 95%. results were further investigated using dotter and mvista., lncrnas were classified into four main categories based on their location relative to protein coding genes: (i) intergenic; (ii) genic-intronic; (iii) genic-exonic and (iv) putative […]


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mVISTA in publications

 (218)
PMCID: 5943242
PMID: 29743507
DOI: 10.1038/s41598-018-25585-4

[…] also contains sequence and gene annotation information for all 28 genotypes. similarly, 45snrdna genes (18s, 5.8s, and 26s) were annotated based on blast analyses and reported reference units. the mvista tool was used to visualize comparative syntenic relationships with other genotypes. complete chloroplast genomes and 40 complete 45snrdna sequences from 28 genotypes were deposited in genbank […]

PMCID: 5885378
PMID: 29618324
DOI: 10.1186/s12864-018-4633-x

[…] (penthoraceae; jx436155) as the reference based on the results of dong et al. [] and soltis et al. []. the sequence identity of the five saxifragaceae chloroplast genomes was plotted using the mvista program with lagan mode []. the cp dna rearrangement analyses of five saxifragaceae chloroplast genomes were performed using mauve alignment []., we determined the four types of repeat […]

PMCID: 5923464
PMID: 29614838
DOI: 10.3390/v10040170

[…] (sias) server (http://imed.med.ucm.es/tools/sias.html). protein secondary structure predictions were performed using psipred v3.3, which is available at http://bioinf.cs.ucl.ac.uk/psipred/ []. the mvista methods of alignment was used for the comparison of concatenated complete coding sequences of prv-3 genome segments with prv-1, -2, and lmbrv []. phylogenetic trees were constructed using […]

PMCID: 5875761
PMID: 29596414
DOI: 10.1371/journal.pone.0192966

[…] using mega 6 software [], and finally the divergence of the p. taeda cp genome from six other pinus species (five from subgenus pinus and one from subgenus strobus) cp genomes was assessed using mvista [] in shuffle-lagan mode and using the p. taeda genome as a reference., repeat sequences, including direct, reverse, and palindromic repeats, were identified within the cp genome using reputer […]

PMCID: 5854438
PMID: 29543905
DOI: 10.1371/journal.pone.0194613

[…] seven cp genomes were deposited in genbank (accession number mg200070, mg211818-mg211823)., a comparative plot consisting of full alignments of the cp genomes with annotations was produced by mvista using f. cirrhosa as the reference. the sequences were aligned using mega 6 [] and then manually adjusted using bioedit software (http://www.mbio.ncsu.edu/bioedit/bioedit.html). subsequently, […]


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mVISTA institution(s)
Department of Computer Science, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada; Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
mVISTA funding source(s)
Supported by grant HL066681, Berkeley-PGA, under the Programs for Genomic Applications, funded by National Heart, Lung and Blood Institute, by HG003988 funded by National Human Genome Research Institute, and performed under Department of Energy Contract DE-AC02-05CH11231, University of California and by NSERC Discovery grant.

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