BoxShade protocols

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BoxShade specifications


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


  • person_outline Kay Hofmann <>
  • person_outline Michael Baron <>


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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  • person_outline Kay Hofmann <>
  • person_outline Michael Baron <>

BoxShade in pipelines

PMCID: 5822839
PMID: 29479499
DOI: 10.7717/peerj.4391

[…] for c9orf72 from all the species studied were aligned using clustalw2 (), a multiple sequence alignment software using default alignment parameters ( boxshade program was used to shade regions of similarity in the aligned sequences ( matcher (one of the emboss programs) was used to locally align […]

PMCID: 5823468
PMID: 29425229
DOI: 10.1371/journal.ppat.1006870

[…] site was used to compare motif identity and similarity with known conserved domains []. sequence alignments were obtained by using clustal omega software [], edited using bioedit and refined using boxshade. the physical-chemical properties of the deduced protein were determined by the protein machine software available at the expasy website ( the disorder […]

PMCID: 5932401
PMID: 29755485
DOI: 10.3389/fpls.2018.00475

[…] anti-actin (691001; mp biomedicals) at 1:5000 and anti-cbp20 (as09 530; agrisera) at 1:1000., 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)., arabidopsis thaliana, gene id: 834443; populus trichocarpa, gene id: 7469563; v. […]

PMCID: 5316894
PMID: 28205520
DOI: 10.1038/ncomms14455

[…] p. falciparum were identified in and protein sequences were aligned using clustalx 2.1 (ref. ) and a visual output of the sequence alignment was generated using the boxshade webserver ( accession numbers of the sequences were as follows: tgme49_215490 (tgnpt1), tgme49_320020, pbanka_020830 (pbnpt1), […]

PMCID: 5381585
PMID: 28201618
DOI: 10.1093/gbe/evx024

[…] last accessed january 11, 2017) was used to generate a “pir” output/alignment of the prophage protein sequences. the “pir” output from clustalw was further aligned using the boxshade server (; last accessed january 11, 2017) to highlight the conserved residues among prophage protein sequences from different species. signal […]

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BoxShade in publications

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

[…] 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 (, the first glcnac (−1) and the last neu5ac (6 and 10) residues of the s2g2 substrate; and the man9glcnac product were modeled using […]

PMCID: 5940834
PMID: 29740074
DOI: 10.1038/s41598-018-25606-2

[…] precursors from other species (see supplementary table  for a list of the sequences) using mafft version 7 (5 iterations, substitution matrix; blosum62) and highlighted using the software boxshade ( with 70% conservation as the minimum for highlighting., radial nerve cords from two specimens of a. rubens were dissected and transferred […]

PMCID: 5917037
PMID: 29725323
DOI: 10.3389/fmicb.2018.00754

[…] 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 […]

PMCID: 5891637
PMID: 29666619
DOI: 10.3389/fmicb.2018.00632

[…] 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., chu_0125 was annotated as an outer membrane peptidoglycan-associated lipoprotein (pal) in ncbi. generally, pal homologs, such as in e. coli, […]

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

[…] 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 ( was used. the identity percentages were calculated using sias server (, to assist […]

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