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GWIPS-viz specifications

Information


Unique identifier OMICS_03728
Name GWIPS-viz
Alternative name Genome Wide Information on Protein Synthesis visualized
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Bacteria
    • Bacillus subtilis
    • Escherichia coli
    • Staphylococcus aureus
  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
    • Plasmodium falciparum
    • Trypanosoma brucei
  • Plants and Fungi
    • Arabidopsis thaliana
    • Saccharomyces cerevisiae
    • Zea mays
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Xenopus laevis

Documentation


Maintainer


  • person_outline Pavel Baranov

Additional information


User Guide: http://gwips.ucc.ie/goldenPath/help/hgTablesHelp.html

Publications for Genome Wide Information on Protein Synthesis visualized

library_books

GWIPS-viz: 2018 update

2018 Nucleic Acids Res
PMCID: 5753223
PMID: 28977460
DOI: 10.1093/nar/gkx790

GWIPS-viz citations

 (3)
library_books

RNA editing by ADAR1 leads to context dependent transcriptome wide changes in RNA secondary structure

2017
Nat Commun
PMCID: 5682290
PMID: 29129909
DOI: 10.1038/s41467-017-01458-8

[…] NormalizedreadcountKD∕Normalizedreadcountcontrol 4TE = NormalizedreadcountRibo-seq∕NormalizedreadcountRNA - seq 5TER = TEKD∕TEcontrol= FCRibo-seq∕FCRNA-seq Ribosome occupancy was calculated using the GWIPS-viz method in Ribogalaxy Meta-gene analysis was done in the span of 150 bases upstream/downstream to translation start/stop sites. […]

library_books

riboviz: analysis and visualization of ribosome profiling datasets

2017
BMC Bioinformatics
PMCID: 5657068
PMID: 29070028
DOI: 10.1186/s12859-017-1873-8

[…] es such as biased codon usage, presence of poly-basic amino-acids, and protein-domain architecture affect the distribution of footprinting reads along a transcript []. Recently, several tools such as GWIPS-viz [], RiboGalaxy [], and RPFdb [] have been developed for both analysis and visualization of ribosome-profiling datasets. While GWIPS-viz and RPFdb use unified pipelines for processing and map […]

library_books

Insights into the mechanisms of eukaryotic translation gained with ribosome profiling

2016
Nucleic Acids Res
PMCID: 5314775
PMID: 27923997
DOI: 10.1093/nar/gkw1190

[…] xt of a whole organism (,) and for the detection of translation quantitative trait loci (,). Ribosome Profiling is now further empowered by a wide spectrum of computational resources. At RiboSeq.Org, GWIPS-viz (,) provides visualizations of genomic alignments for publicly available RiboSeq data aligned to the genomes of a dozen of organisms and RiboGalaxy () allows researchers to analyse their dat […]

Citations

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GWIPS-viz institution(s)
School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
GWIPS-viz funding source(s)
Supported by Science Foundation Ireland (12/IA/1335) and the Wellcome Trust (094423).

GWIPS-viz review

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Anonymous user #31413

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Dataset
In the recent ten years many of ribosome profiling (RP) assays were done.
This is a web tool to visualize ribosome profiling data. Its contains tens of RP studies in 24 organisms, including model organisms like mouse, worm, yeast and of course Human.
I finds this web tool very useful.
You can enter a location on the DNA or query gene and get out pot of the RP reads in this area.