mVISTA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool mVISTA
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This map represents all the scientific publications referring to mVISTA per scientific context
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Protocols

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 citations

 (276)
library_books

Re exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences

2018
Sci Rep
PMCID: 5943242
PMID: 29743507
DOI: 10.1038/s41598-018-25585-4

[…] er 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 ( […]

library_books

The Complete Plastome Sequences of Seven Species in Gentiana sect. Kudoa (Gentianaceae): Insights Into Plastid Gene Loss and Molecular Evolution

2018
Front Plant Sci
PMCID: 5938401
PMID: 29765380
DOI: 10.3389/fpls.2018.00493

[…] to sect. Cruciata, were obtained for comparative analysis from the National Center for Biotechnology Information. Genome comparisons were performed to identify the differences among the 11 taxa using mVISTA () and Geneious Basic 5.6.4 (). To identify divergence hotspots, nucleotide diversity (Pi) was determined using DnaSP V. 5.10 (). […]

call_split

The chloroplast genome of Cerasus humilis: Genomic characterization and phylogenetic analysis

2018
PLoS One
PMCID: 5919044
PMID: 29694421
DOI: 10.1371/journal.pone.0196473
call_split See protocol

[…] To investigate the differences between the C. humilis genome sequence and those of the other members of the same genus, we used the LAGAN alignment strategy as implemented in the mVISTA software to compare the whole genome sequence of ten species of Prunus with C. humilis, using C. humilis as reference [] (http://genome.lbl.gov/cgi-bin/VistaInput?num_seqs=2). In addition, the […]

library_books

The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae

2018
PLoS One
PMCID: 5919006
PMID: 29694416
DOI: 10.1371/journal.pone.0196069

[…] ed on the Kimura 2-parameter model using MEGA 7.0.21 []. Standard error estimate(s) were obtained using bootstrap (1,000 replicates). Complete plastid genome sequences were compared and aligned using mVISTA online tools [], while the expansion and contraction of the inverted repeat (IR) regions at junction sites was examined and plotted using IRscope []. We identified and located repeat sequences […]

library_books

Chloroplast genome analyses and genomic resource development for epilithic sister genera Oresitrophe and Mukdenia (Saxifragaceae), using genome skimming data

2018
BMC Genomics
PMCID: 5885378
PMID: 29618324
DOI: 10.1186/s12864-018-4633-x

[…] inense (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 []. […]

library_books

Molecular and Antigenic Characterization of Piscine orthoreovirus (PRV) from Rainbow Trout (Oncorhynchus mykiss)

2018
Viruses
PMCID: 5923464
PMID: 29614838
DOI: 10.3390/v10040170

[…] es (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 the R […]


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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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