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VIPS specifications

Information


Unique identifier OMICS_17979
Name VIPS
Alternative name Viral IRES Prediction System
Interface Web user interface
Restrictions to use None
Input data A DNA or RNA sequence.
Computer skills Basic
Stability No
Maintained No

Documentation


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Publication for Viral IRES Prediction System

VIPS citations

 (4)
library_books

Discovery of Culex pipiens associated tunisia virus: a new ssRNA(+) virus representing a new insect associated virus family

2018
Virus Evol
PMCID: 5763275
PMID: 29340209
DOI: 10.1093/ve/vex040

[…] ail was performed using PolyApred (). RNA motifs and cis-regulatory elements such as tRNA-like structures were searched using RegRNA 2.0 (). Internal ribosomal entry sites (IRES) were predicted using Viral IRES Prediction System (VIPS) with default parameters ().BLAST searches (e-value threshold=1) were performed against Plasmodium genomes available in PlasmoDB () (release 2015/07/23) to detect ho […]

library_books

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

2018
Front Microbiol
PMCID: 5758548
PMID: 29354101
DOI: 10.3389/fmicb.2017.02582

[…] ops and/or pseudoknots (Dreher, ; Lozano et al., ). Limited progress has been made in development of automated pipelines for IRES prediction, however, two specialized webservers are available, namely VIPS (Hong et al., ) and IRESPred (Kolekar et al., ). Both VIPS and IRESPred predict IRES based on known IRES sequences and structures. In particular, IRESPred looks for the binding sequence motifs of […]

library_books

Genome wide analysis of circular RNAs in prenatal and postnatal pituitary glands of sheep

2017
Sci Rep
PMCID: 5700919
PMID: 29170496
DOI: 10.1038/s41598-017-16344-y

[…] translation of an mRNA sequence without a 5′-cap structure. If a circRNA has at least one IRES element, then it may be able to encode a protein. To annotate the coding potential of sheep circRNAs, a Viral IRES Prediction System (VIPS) was employed to predict the IRES element in the sequence of each sheep circRNAs. In addition, the longest ORFs were predicted for each circRNA using DNAman. Any fra […]

library_books

The Evolution of LINE 1 in Vertebrates

2016
Genome Biol Evol
PMCID: 5381506
PMID: 28175298
DOI: 10.1093/gbe/evw247

[…] ce of an IGR is the effect this region will have on the translation of the ORFs. The IGRs differ considerably in length and base composition, yet the two IRES detection programs we used (IRESPred and VIPS) suggest the presence of IRES in the vast majority of elements with long IGR. Considering the uncertainty of in silico IRES predictions, it will be necessary to validate experimentally the presen […]

Citations

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VIPS institution(s)
Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li, Taiwan; Center for Nanotechnology and Institute of Biomedical Technology, Chung Yuan Christian University, Chung-Li, Taiwan; R&D Center of Membrane Technology, Chung Yuan Christian University, Chung-Li, Taiwan; Information Management Department, Ming Chuan University, Guishan Township, Taoyuan, County, Taiwan
VIPS funding source(s)
Supported by the National Science Counsel of Taiwan (NSC-99-2632-M-033-001-MY3) and the R&D Center of Membrane Technology, Chung Yuan Christian University, Chung-Li, Taiwan.

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