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Protocols

PLEXY specifications

Information


Unique identifier OMICS_16763
Name PLEXY
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A snoRNA sequence with annotated box-motifs and a list of potential target RNAs.
Input format FASTA
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Requirements
RNAPLEX
Maintained Yes

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Maintainer


  • person_outline Stephanie Kehr

Publication for PLEXY

PLEXY citations

 (17)
library_books

A comprehensive benchmark of RNA–RNA interaction prediction tools for all domains of life

2016
Bioinformatics
PMCID: 5408919
PMID: 27993777
DOI: 10.1093/bioinformatics/btw728

[…] and evolutionary conservation to predict interactionsSome RNA–RNA interaction prediction tools are developed to achieve a specific task or to predict very specific group of interactions. For example, PLEXY is designed for C/D snoRNAs (), RNAsnoop () for H/ACA snoRNAs and TargetRNA () for bacterial sRNAs (E. coli and Salmonella). In this study, we tried to assess the versatility of prediction tools […]

library_books

High throughput identification of C/D box snoRNA targets with CLIP and RiboMeth seq

2016
Nucleic Acids Res
PMCID: 5389715
PMID: 28031372
DOI: 10.1093/nar/gkw1321

[…] PLEXY is a tool for the transcriptome-wide prediction of C/D box snoRNA targets. It uses nearest-neighbor energy parameters to compute thermodynamically stable C/D-box snoRNA - target RNA interactions […]

library_books

An updated human snoRNAome

2016
Nucleic Acids Res
PMCID: 4914119
PMID: 27174936
DOI: 10.1093/nar/gkw386

[…] ions based on state-of-the-art computational methods () with experimental data on snoRNA-guided RNA modifications. The computational target prediction follows three main steps. First, RNAsnoop () and Plexy () are used to predict human targets based on primary sequence features, secondary structure of the snoRNA, the accessibility of the target region, and the predicted minimum free energy of the s […]

library_books

The non coding RNA composition of the mitotic chromosome by 5′ tag sequencing

2016
Nucleic Acids Res
PMCID: 4889943
PMID: 27016738
DOI: 10.1093/nar/gkw195

[…] shed snoRNA sequence characteristics using SnoReport and indeed identified 21 that are possibly novel C/D box snoRNA (Supplementary Table S8). Further inspection of these putatively novel snoRNA with PLEXY resulted in the identification of the potential target of these snoRNAs for 17 of the predicted CD snoRNAs (Supplementary Figure S6, Table S5). While future efforts are needed to confirm these p […]

call_split

Optogenetic control of nuclear protein export

2016
Nat Commun
PMCID: 4748110
PMID: 26853913
DOI: 10.1038/ncomms10624
call_split See protocol

[…] amplicons were digested with BsmBI and ligated, thereby generating construct pDN136.To simplify cloning of mCherry-LEXY-tagged proteins of interest, we generated two golden gate entry vectors, namely pLEXY (pDN137) and pNLS-LEXY (pDN138). These vectors encode a CMV promoter-driven mCherry-LEXY expression cassette preceded by a bacterial toxin-encoding gene (ccdB). The ccdB is flanked by BpiI (BbsI […]

library_books

A comprehensive comparison of general RNA–RNA interaction prediction methods

2015
Nucleic Acids Res
PMCID: 4838349
PMID: 26673718
DOI: 10.1093/nar/gkv1477

[…] gical class of interactions. Various existing tools for miRNA prediction already pursue this, taking advantage of binding motifs and highly specific interactions lengths. There are also tools such as PLEXY (), which can accurately predict C/D snoRNA binding sites by using nucleotide sequence motifs to narrow down the window of prediction. Alternatively, recent advancements have been made in high-t […]

Citations

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PLEXY institution(s)
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria; Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany; RNomics Group, Fraunhofer Institute Cell Therapy and Immunology, Leipzig, Germany; Center for non-coding RNAs in Technology and Health (RTH), University of Copenhagen, Copenhagen, Denmark; The Santa Fe Institute, Santa Fe, NM, USA
PLEXY funding source(s)
Supported by European Union under the auspices of the FP-7 QUANTOMICS project.

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