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BoxShade specifications

Information


Unique identifier OMICS_19792
Name BoxShade
Interface Web user interface
Restrictions to use None
Programming languages Pascal
Computer skills Basic
Version 3.21
Maintained Yes

Maintainers


  • person_outline Kay Hofmann
  • person_outline Michael Baron

Information


Unique identifier OMICS_19792
Name BoxShade
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Pascal
Computer skills Advanced
Version 3.2.3
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Kay Hofmann
  • person_outline Michael Baron

BoxShade citations

 (362)
library_books

Structural basis for the recognition of complex type N glycans by Endoglycosidase S

2018
Nat Commun
PMCID: 5951799
PMID: 29760474
DOI: 10.1038/s41467-018-04300-x

[…] a. Protein pocket volume was calculated using HOLLOW. Z-score values were produced by using DALI. Domain interface analysis was performed using PISA. Conserved and similar residues were labeled using BoxShade server (http://embnet.vital-it.ch/software/BOX_form.html). […]

call_split

Discovery and functional characterisation of a luqin type neuropeptide signalling system in a deuterostome

2018
Sci Rep
PMCID: 5940834
PMID: 29740074
DOI: 10.1038/s41598-018-25606-2
call_split See protocol

[…] Yamide-type precursors from other species (see supplementary TableĀ  for a list of the sequences) using MAFFT version 7 (5 iterations, substitution matrix; BLOSUM62) and highlighted using the software BOXSHADE (www.ch.embnet.org/software/BOX_form.html) with 70% conservation as the minimum for highlighting. […]

library_books

Identification and Characterization of a Novel Hepta Segmented dsRNA Virus From the Phytopathogenic Fungus Colletotrichum fructicola

2018
Front Microbiol
PMCID: 5917037
PMID: 29725323
DOI: 10.3389/fmicb.2018.00754

[…] to identify the conserved domains of the full-length cDNA virus sequences. MAFFT software () was used for multiple nucleotide and amino acid sequence alignments, and the results were visualized using BoxShade. Phylogenetic trees were constructed using the maximum likelihood method in Molecular Evolutionary Genetics Analysis (MEGA) software 7 (). Reference sequences of the viruses used for comparat […]

call_split

A Role of U12 Intron in Proper Pre mRNA Splicing of Plant Cap Binding Protein 20 Genes

2018
Front Plant Sci
PMCID: 5932401
PMID: 29755485
DOI: 10.3389/fpls.2018.00475
call_split See protocol

[…] Comparison between DNA and protein sequences was carried out using bioinformatics tools: ClustalW2 and BoxShade. Sequencing results were assembled together using the ContigExpress program from Vector NTI (Invitrogen). […]

call_split

Deletion of a Gene Encoding a Putative Peptidoglycan Associated Lipoprotein Prevents Degradation of the Crystalline Region of Cellulose in Cytophaga hutchinsonii

2018
Front Microbiol
PMCID: 5891637
PMID: 29666619
DOI: 10.3389/fmicb.2018.00632
call_split See protocol

[…] genome sequence of C. hutchinsonii was obtained from the NCBI database. CLUSTALW was used for the multiple alignment of related Pals. T-COFFEE and MUSCLE were applied to verify the CLUSTALW results. BoxShade was a tool to shade multiple alignment files. […]

library_books

Proteomic endorsed transcriptomic profiles of venom glands from Tityus obscurus and T. serrulatus scorpions

2018
PLoS One
PMCID: 5862453
PMID: 29561852
DOI: 10.1371/journal.pone.0193739

[…] cleotide sequences of each individual toxin were translated into amino acid sequences and aligned by ClustalW [] using default parameters, manually edited using Seaview [] and, for presenting figures Boxshade (http://www.ch.embnet.org/software/BOX_form.html) was used. The identity percentages were calculated using SIAS server (http://imed.med.ucm.es/Tools/sias.html). […]

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