eBioX protocols

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eBioX specifications

Information


Unique identifier OMICS_08913
Name eBioX
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Mac OS
License GNU General Public License version 2.0
Computer skills Medium
Stability No
Maintained No

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Publication for eBioX

eBioX in pipelines

 (5)
2016
PMCID: 4938498
PMID: 27391425
DOI: 10.1371/journal.pone.0158919

[…] were performed as described above., the nucleotide sequence of the full-length cdna obtained was analyzed for homology by blastn at the ncbi website (http://blast.ncbi.nlm.nih.gov/blast.cgi). ebiox (v1.5.1) software was used for searching polyadenylation sites and for translating the open reading frame (orf). homology analysis of the protein sequence was carried out with blastp […]

2013
PMCID: 3711925
PMID: 23845108
DOI: 10.1186/1471-2164-14-470

[…] the protein coding region for each ensembl gene model to the mrna sequence derived from the secondary genomic alignment (i.e. the allelic variant). all sequence analyses were performed using the ebiox (1.5.1) suite of analysis tools []. specifically, pairwise alignments of protein and mrna sequences were estimated using a smith-waterman local alignment algorithm []; multiple sequence […]

2013
PMCID: 3826655
PMID: 24131955
DOI: 10.1038/ncomms3601

[…] were compared with the sequence of strain 630 (am180355) and the shotgun sequence of strain cd37 (ahjj01000000) using the artemis comparison tool. snp analysis was performed by alignment using ebiox version 1.51. sequence of the chromosomal dna used to compare the donor- and recipient-specific dna in the transconjugants is provided in . sequence at the junctions between the chromosome […]

2010
PMCID: 2900272
PMID: 20546574
DOI: 10.1186/1471-2148-10-176

[…] ones having the lowest e- values) from a variety of major bacterial groups were retrieved and aligned with eukaryotic γ-type ca homologs using muscle v.3.6 []. the alignment was edited manually with ebiox and was then used to reconstruct the maximum likelihood phylogenetic tree using raxml-hpc [] under the wag + γ model (using the protgammawagf option) with 25 categories of substitution rate […]

2010
PMCID: 3022682
PMID: 21172023
DOI: 10.1186/1743-422X-7-369

[…] http://www.hiv.lanl.gov/content/sequence/gene_cutter/cutter.html. hxb2 was included in each msa to identify the selected regions. msas were further edited manually using msa editors bioedit and ebiox, and analyzed in clc dna workbench http://www.clcbio.com (aarhus, denmark)., sequences from naïve isolates were retrieved from los alamos hiv databases. msas were generated as mentioned […]


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eBioX in publications

 (25)
PMCID: 5578954
PMID: 28860563
DOI: 10.1038/s41598-017-10717-z

[…] (both directions) employing the bigdye terminator sequencing kit version 3.1, and applied biosystems 3730xl analyzer (foster city, ca, usa). the sequencing chromatograms were visualized with ebiox version 1.5.1 (output examples of hotspot mutations shown in supplementary fig. ). previously published kras mutation data were compared with the new mutational data for 250 overlapping cases […]

PMCID: 5495683
PMID: 28605891
DOI: 10.3961/jpmph.17.013

[…] ltd., suffolk, uk) or ortho-phthalaldehyde (ethicon inc., irvine, ca, usa) from sedimentation, rinsed with distilled water, and dried. the handle is disinfected using disinfection wipes (ebiox ltd., cheshire, uk). blades are usually packed and sealed in synthetic resin packing materials or left unpacked with the handles. in this case, the instrument would be contaminated by the cart […]

PMCID: 4994000
PMID: 27549344
DOI: 10.1038/srep31449

[…] the biocl1−xbrx solid solutions and largest for the biof1−xix solid solutions., to describe the miscibility of the biox1−xyx solid solutions, the formation enthalpy was also calculated:, , where ebiox and ebioy are the total energies of pure biox and bioy with the same size of supercell, and ebiox1−xyx is the total energy of the biox1−xyx solid. the calculated results are shown in . […]

PMCID: 4970327
PMID: 27458136
DOI: 10.1083/jcb.201603105

[…] baseline mdv levels, respectively (r2 = 0.98 for control sirna; r2 = 0.91 for sistx17). diagrams of the structure of the snare tetrad and the r-snare sequence alignment were created with pymol and ebiox, respectively., fig. s1 examines the effect of stx17 depletion on the targeting of other mdv populations to other cellular destinations. fig. s2 demonstrates that vamp7 and vamp8 localize […]

PMCID: 4938498
PMID: 27391425
DOI: 10.1371/journal.pone.0158919

[…] instructions. sequence homology for all the sequenced pcr products was confirmed by blastn at the ncbi web site (http://blast.ncbi.nlm.nih.gov/blast.cgi). fragment assembly was made with the ebiox (v1.5.1) software for macintosh. despite the several clones sequenced (24 from eight different degenerated primer combinations) from different individuals p. argus, this procedure allowed […]


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eBioX institution(s)
The Linnaeus Centre for Bioinformatics, Uppsala University, Biomedical centre, Uppsala, Sweden

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