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KnotInFrame specifications

Information


Unique identifier OMICS_06333
Name KnotInFrame
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Information


Unique identifier OMICS_06333
Name KnotInFrame
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for KnotInFrame

KnotInFrame citations

 (6)
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

[…] ing, and current tools are <5% accurate (Leamy et al., ). This may be improved by including experimental data (Hajdin et al., ).These ribosomal frameshifting sites can be predicted specifically using KnotInFrame (Theis et al., ). Others have used more general software, e.g., RNA Shapes Studio (Janssen and Giegerich, ) as was done for Zika virus, or combination of prediction programs as was used to […]

library_books

An RNA Virome Associated to the Golden Orb Weaver Spider Nephila clavipes

2017
Front Microbiol
PMCID: 5660997
PMID: 29118750
DOI: 10.3389/fmicb.2017.02097

[…] complementary virus sequence termini were assessed with the RNAcofold web server http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAcofold.cgi. Ribosomal frameshifting events were predicted using the KnotInFrame tool https://bibiserv.cebitec.uni-bielefeld.de/knotinframe. The potential functions of the ORFs products were predicted by the annotated data and similarity with known viral proteins. Viru […]

call_split

West Nile alternative open reading frame (N NS4B/WARF4) is produced in infected West Nile Virus (WNV) cells and induces humoral response in WNV infected individuals

2012
Virol J
PMCID: 3574045
PMID: 23173701
DOI: 10.1186/1743-422X-9-283
call_split See protocol

[…] 384 full genomes of WNV were retrived from gene bank and aligned with BioNumerics software package (version 6.5 Applied-Maths, Belgium). Genomes were further analized by KnotInFrame software (http://bibiserv.techfak.uni-bielefeld.de/knotinframe/) to predict ribosomal −1 frameshift sites with a pseudoknot strucuture. […]

library_books

On programmed ribosomal frameshifting: the alternative proteomes

2012
Front Genet
PMCID: 3500957
PMID: 23181069
DOI: 10.3389/fgene.2012.00242

[…] mmell et al., ). This approach identified over 200 putative programmed ribosomal frameshifting events. For identification of pseudoknots and slippery sequences in the genome databases such as RECODE, KnotInFrame, PRFdb, and FSdB are very useful (Table ).RECODE provides information about programmed frameshifting, read-through and bypassing, based on published results in the literature (Baranov et a […]

library_books

Novel Bacteriophages Containing a Genome of Another Bacteriophage within Their Genomes

2012
PLoS One
PMCID: 3398947
PMID: 22815791
DOI: 10.1371/journal.pone.0040683

[…] ploit the programmed frameshift mechanism for gene expression and the majority of frameshift candidates appear to use a -1 frameshift . However, no canonical -1 frameshift signal has been detected by KnotInFrame, a tool for the prediction of ribosomal frameshift events . Alternatively, ORF55 and ORF56 might encode two distinct proteins possibly forming a two-subunit complex. ORF40 of SpaA1 encodes […]

library_books

Strain specific copy number variation in the intelectin locus on the 129 mouse chromosome 1

2011
BMC Genomics
PMCID: 3048546
PMID: 21324158
DOI: 10.1186/1471-2164-12-110

[…] edicted transcripts were predicted with the RNASPL program of the Softberry web server [] to check for alternative splicing. Potential frame-shifting in the transcripts were checked with the web tool KnotInFrame []. Repeat elements on the locus were identified using the program RepeatMasker (v3.2.7) []. […]

Citations

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KnotInFrame institution(s)
Faculty of Technology, Bielefeld University, Bielefeld, Germany

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