MView protocols

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MView specifications

Information


Unique identifier OMICS_15907
Name MView
Alternative name EBI-MView
Interface Web user interface
Restrictions to use None
Input data A protein sequence or a DNA sequence.
Input format BLAST, FASTA, PEARSON, CLUSTAL, MSF, PIR, HSSP
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Information


Unique identifier OMICS_15907
Name MView
Alternative name EBI-MView
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A protein sequence or a DNA sequence.
Input format BLAST, FASTA, PEARSON, CLUSTAL, MSF, PIR, HSSP
Output format HTML, FASTA, CLUSTAL, MSF, PIR, RDB
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


MView in pipelines

 (4)
2016
PMCID: 5148604
PMID: 27874830
DOI: 10.7554/eLife.19130.019

[…] and stop codons) using exonerate (). within each ortholog sets, multiple sequence alignment was performed using muscle (rrid:scr_011812) () and the percentage of sequence identity was assessed by mview (). for the sequence fragments or missing sequences due to poor coverage, they were filled up using the consensus. we confirmed the filling up procedure did not significantly affect the read […]

2015
PMCID: 4410388
PMID: 25927077
DOI: 10.1126/sciadv.1400234

[…] by total blast score, and the ncbi genomic workbench was used to automatically parse repeats within the top-scoring reads. phylogenies were constructed using mafft with default parameters. the ebi mview sequence editor was used for alignment display., we thank h. malik, p. green, p. talbert, a. drinnenberg, and f. steiner for discussions and critical comments. funding: supported by nih r01 […]

2014
PMCID: 4047054
PMID: 24901469
DOI: 10.1371/journal.pone.0099074

[…] conservation was analyzed using ali2d ., for multiple sequence alignment, flz and zf-fcs domain sequences were retrieved from pfam. they were aligned with clustal x 2.0 and visualized using mview , . pair wise hmm logo comparison was done using logomat-p . fold recognition of flz domain was done using phyre v 0.2 . sequence logo was generated using weblogo . the domain organization […]

2014
PMCID: 4082311
PMID: 24870228
DOI: 10.1038/nature13420

[…] with the scipy python package (http://www.scipy.org, version 0.9.0) within the “stats” library. multiple sequence alignment for indels visualization and plot was performed with clustalw2 and mview (http://bio-mview.sourceforge.net/)., peripheral blood and bone marrow samples from a subject with scid-x1 were obtained according to the guidelines of the medical ethics committee […]


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MView in publications

 (28)
PMCID: 5943563
PMID: 29774040
DOI: 10.3389/fpls.2018.00580

[…] binary vectors, bifc vectors, and venus cdna, klu-4 seeds, respectively., http://www.arabidopsis.org/ , https://www.r-project.org/ , http://bar.utoronto.ca/ntools/cgi-bin/ntools_multiplealign_w_mview.cgi , http://travadb.org/ , the supplementary material for this article can be found online at: […]

PMCID: 5854411
PMID: 29505558
DOI: 10.1371/journal.pgen.1007251

[…] of the corresponding plot and displayed as above or below the mean., crts sequences of vibrionaceae in were found with blast []. the alignment was done with clustalomega [] and the layout with mview []. additionally, crts sites in 114 vibrionaceae from ncbi were found with fuzznuc (http://www.hpa-bioinfotools.org.uk/pise/fuzznuc.html) by using the sequence cagnatatgtaactnatgctttcgg […]

PMCID: 5727874
PMID: 29233099
DOI: 10.1186/s12864-017-4364-4

[…] []. identified snps were incorporated into the reference sequences from ensembl, and translated to proteins using the expasy online translate tool [], aligned using clustalw [], and visualized using mview [] through the embl-ebi online web services []. homologous sequences were identified using ncbi’s blastn and blastp []. correlation analysis dendrograms were created in r by running pvclust [] […]

PMCID: 5549716
PMID: 28792538
DOI: 10.1371/journal.pone.0182782

[…] to regulate dgc activity and bpegreg may interact with other dgcs to form mixed signaling teams., protein sequences were aligned using ebi-mafft [, ]. the alignment was visualized by using ebi-mview [, ]. the homology model of bpegreg was created previously []. visualization of the locations of the critical residues was carried out using ucsf chimera []., the ecgreg (genbank accession no. […]

PMCID: 5472580
PMID: 28620186
DOI: 10.1038/s41598-017-02743-8

[…] structures were visualized and analyzed using pymol pdb viewer (pymol.org). antigenic epitopes predicted for s1133 arv strain were compared with antigenic sequences predicted for our isolates using mview(http://www.ebi.ac.uk/tools/msa/mview/). in addition, the sigma b antigenic epitopes were predicted using emboss-antigenic (http://www.bioinformatics.nl/cgi-bin/emboss/antigenic) and kolaskar […]


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