LogoBar specifications

Information


Unique identifier OMICS_09361
Name LogoBar
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 0.912
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Thomas R. Bürglin <>

Publication for LogoBar

LogoBar in publications

 (6)
PMCID: 5320794
PMID: 28222763
DOI: 10.1186/s13104-017-2429-8

[…] the esl-reformat and hmmbuild programs, respectively, which are part of the hmmer tool version 3 []. from the multiple protein alignment, a protein sequence logo was created using the java program logobar version 0.912 []. the frequency of the residues was represented by the size of the letter. amino acids are grouped and colored using the following (cinema) color scheme, in which the polar […]

PMCID: 4448998
PMID: 26024448
DOI: 10.1371/journal.pone.0126947

[…] endrov [], that we developed to conduct a survey of the embryonic expression patterns of many of these genes with high spatio-temporal resolution., sequence analyses and protein logo creation with logobar were carried out as previously described. [, –]. to generate an updated list of homeobox genes in c. elegans, we conducted psi-blast searchers of the c. elegans protein sequences in genbank. […]

PMCID: 3036627
PMID: 21272360
DOI: 10.1186/1743-422X-8-44

[…] finding and facilitates the management of diversity in sequences., the bioperl[] modules were used for automating the analysis of the alignments using different tools from emboss like geecee [], logobar [], infoalign [], cons [] and plotcon []. scripts were written for each of these tools and run under the biolinux operating environment []. these scripts are available upon request. […]

PMCID: 2644675
PMID: 19193230
DOI: 10.1186/1471-2148-9-31

[…] with the default parameters [,]. a bar chart representation was used in order show the frequency of each residue at every position of the alignment of vertebrate h2a.z-1 and h2a.z-2 forms using the logobar program []. the 3d structures of h2a.z-1 and h2a.z-2 proteins from vertebrates as well as h2a.z-e from early chordates were modeled using the coordinates determined for the crystal structure […]

PMCID: 2663770
PMID: 19192292
DOI: 10.1186/1756-0500-2-16

[…] group for trypanosomatids, as the latter do not contain plastids. mitoprot ii contains no option for assessing plastid localization. the consensus e. gracilis mtp profile was generated using logobar-0.9.12 [] from a de-gapped alignment of the 30-most n-terminal residues from 107 predicted e. gracilis mitochondrion-targeted proteins., conserved domains were identified by searching […]


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LogoBar institution(s)
Department of Biosciences at Novum, and Center for Genomics and Bioinformatics, Karolinska Institutet Alfred Nobels, Huddinge, Sweden; Department of Life Sciences, Södertörns högskola Alfred Nobels, Huddinge, Sweden; International Master's Programme in Bioinformatics, Chalmers University of Technology Gothenburg, Sweden

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