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GCView specifications

Information


Unique identifier OMICS_24527
Name GCView
Interface Web user interface
Restrictions to use None
Input data A protein sequence, a protein GI or UniProt identifiers and forwarded homology search jobs.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Dirk Linke

Publication for GCView

GCView citations

 (5)
library_books

Genomic insights of Pannonibacter phragmitetus strain 31801 isolated from a patient with a liver abscess

2017
PMCID: 5727363
PMID: 28857514
DOI: 10.1002/mbo3.515

[…] gous Groups, and WebMGA programs (Markowitz et al., ; Wu, Zhu, Fu, Niu, & Li, ; Markowitz et al., ; Overbeek et al., ; Galperin, Makarova, Wolf, & Koonin, ). A circular genome map was generated using GCView based on all predicted CDS information, tRNAs/rRNAs, GC content, and gene cluster information (Grant & Stothard, ). The multidrug resistance genes were predicted using both CARD database (McArt […]

library_books

The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis

2017
PLoS One
PMCID: 5291543
PMID: 28158318
DOI: 10.1371/journal.pone.0171264

[…] variation of the Ulmus species, we used the chloroplast genome of U. pumila as a reference and analyzed single nucleotide variations (SNV) and indel variations in their chloroplast genomes using the GCView Server (http://stothard.afns.ualberta.ca/cgview_server/index.html) (). U. davidiana var. japonica had the most mutation sites (total, 360; SNV, 286; indel, 74), followed by U. davidiana (total, […]

library_books

The Type III Secretion System (T3SS) is a Determinant for Rice Endophyte Colonization by Non Photosynthetic Bradyrhizobium

2015
PMCID: 4676552
PMID: 26582551
DOI: 10.1264/jsme2.ME15080

[…] . Predictions of gene regions and annotation were performed using MiGAP (http://www.migap.org/index.php/en/about-migap). A circular genome map showing the GC skew and GC content was created using the GCview Server (http://stothard.afns.ualberta.ca/cgview_server).The genome sequences of Bradyrhizobium sp. SUTN9-2 (accession number LAXE00000000) were compared with the whole genome of B. diazoefficie […]

call_split

A Trimeric Lipoprotein Assists in Trimeric Autotransporter Biogenesis in Enterobacteria*

2013
PMCID: 3953254
PMID: 24369174
DOI: 10.1074/jbc.M113.513275
call_split See protocol

[…] The genomic context of sadB and its paralogs was investigated using GCView () in the MPI Bioinformatics Toolkit (). Sequences homologous to SadB or YajI were collected from up to three rounds of PSI-BLAST () and forwarded to GCView for genomic context lookup and inspe […]

library_books

Type V secretion: mechanism(s) of autotransport through the bacterial outer membrane

2012
PMCID: 3297439
PMID: 22411980
DOI: 10.1098/rstb.2011.0208

[…] sport of HMW1 and HMW2, respectively.The genes encoding TpsA and TpsB proteins are organized into operons, where the TpsB gene usually precedes the TpsA gene (a). However, genomic context analysis by GCView [] shows that in some cases, the order is reversed (a). Although it would in principle be conceivable that a single TpsB was responsible for the transportation of several different TpsA protein […]

Citations

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GCView institution(s)
Max Planck Institute for Developmental Biology, Protein Evolution, Tubingen, Germany
GCView funding source(s)
Supported by the Departmental funding of the Max Planck Society.

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