GenomeView protocols

View GenomeView computational protocol

GenomeView statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Genome visualization chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

GenomeView specifications

Information


Unique identifier OMICS_00913
Name GenomeView
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainers


  • person_outline Yves Van de Peer <>
  • person_outline Thomas Abeel <>

Additional information


http://genomeview.org/manual/Main_Page http://genomeview.org/content/advanced-manual

Publication for GenomeView

GenomeView in pipelines

 (3)
2017
PMCID: 5449364
PMID: 28560587
DOI: 10.1186/s12284-017-0164-3

[…] and searched for presence of lectin genes. duplicated genes with a ks (synonymous substitution) value higher than 1.0 were omitted., the genomic structure of the oseul genes was analyzed in genomeview (abeel et al. ) using the japonica rgap release seven sequence. visual representation of the genomic structure of the eul genes was made in ibs 1.0.1 (http://ibs.biocuckoo.org/). sequences […]

2017
PMCID: 5601477
PMID: 28916813
DOI: 10.1038/s41598-017-11866-x

[…] transcripts cannot be definitively assigned to the nuclear genome of p. pemaquidensis ccap 1560/4., gene models for the host and endosymbiont nuclear genomes were viewed and edited manually with genomeview and various in-house perl scripts. gene annotations were performed automatically using the webmga server to generate kog, kegg, pfam, go and ec predictions. amino acid sequences were also […]

call_split

IMA Genome F 8

2017
PMCID: 5729718
PMID: 29242781
DOI: 10.5598/imafungus.2017.08.02.10

[…] sequencing was performed at bgi (hk) using hiseq2000 100bp pe sequencing. rnaseq reads were mapped to the c. zeina reference genome using tophat2 (). manual gene finding of 150 c. zeina genes using genomeview () was guided by blast () alignments of c. zeae-maydis (jgi) genes to the c. zeina reference genome together with c. zeina transcriptome mapping information for gene and splice site […]


To access a full list of citations, you will need to upgrade to our premium service.

GenomeView in publications

 (17)
PMCID: 5601477
PMID: 28916813
DOI: 10.1038/s41598-017-11866-x

[…] transcripts cannot be definitively assigned to the nuclear genome of p. pemaquidensis ccap 1560/4., gene models for the host and endosymbiont nuclear genomes were viewed and edited manually with genomeview and various in-house perl scripts. gene annotations were performed automatically using the webmga server to generate kog, kegg, pfam, go and ec predictions. amino acid sequences were also […]

PMCID: 5608401
PMID: 28892507
DOI: 10.1371/journal.pbio.2003769

[…] also compared against the ncbi protein database as well as the protein data set for st7 using blastp. signalp results were generated using a locally installed version of signalp. the genome browser genomeview [] was chosen for annotation because of its relative ease in setting up and populating with information via gff files and the ability to alter the information using custom scripts. […]

PMCID: 5501885
PMID: 28725555
DOI: 10.1016/j.gdata.2017.07.003

[…] the ncbi non redundant database, to yield a total of 5326 cds (). some of the gene models were manually curated on the orcae platform (http://bioinformatics.psb.ugent.be/orcae/; ) and visualized on genomeview (http://genomeview.org; ). interestingly, an arginase, whose gene had no equivalent in saccharomycotina yeasts, but which presented strong sequence similarities with those of penicillium […]

PMCID: 5449364
PMID: 28560587
DOI: 10.1186/s12284-017-0164-3

[…] and searched for presence of lectin genes. duplicated genes with a ks (synonymous substitution) value higher than 1.0 were omitted., the genomic structure of the oseul genes was analyzed in genomeview (abeel et al. ) using the japonica rgap release seven sequence. visual representation of the genomic structure of the eul genes was made in ibs 1.0.1 (http://ibs.biocuckoo.org/). sequences […]

PMCID: 5249044
PMID: 28105939
DOI: 10.1186/s12864-016-3357-z

[…] visualization of read alignment files was made by tablet 1.13.07.31 []., an automatic annotation of mitochondrial genome sequences was performed using the mitos pipeline with default settings []. genomeview browser [] was used for visualization of annotation files and manual correction of gene boundaries. pcgs boundaries were verified by comparison with the orthologs of other amphipods […]


To access a full list of publications, you will need to upgrade to our premium service.

GenomeView institution(s)
Department of Plant Systems Biology, VIB, Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biomedical Engineering and Microbiology, Boston University, Boston, MA, USA; National Emerging Infectious Diseases Lab, Boston University, Boston, MA, USA
GenomeView funding source(s)
Supported by Research Foundation Flanders (FWO); Belgian American Education Foundation; Ghent University (Multidisciplinary Research Partnership ‘‘Bioinformatics: from nucleotides to networks’’); Interuniversity Attraction Poles Programme (IUAP P6/ 25), initiated by the Belgian State, Science Policy Office (BioMaGNet).

GenomeView reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GenomeView