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 in publications

 (16)
PMCID: 5408919
PMID: 27993777
DOI: 10.1093/bioinformatics/btw728

[…] evolutionary conservation to predict interactions, some 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 […]

PMCID: 5389715
PMID: 28031372
DOI: 10.1093/nar/gkw1321

[…] captured in chimeras from false positives, we developed an additional model as follows. we extracted putative target sites that were captured in multiple chimeras with the same snorna and had a plexy-predicted energy of interaction () lower than -12 kcal/mol. from the combined clip experiments we identified 362 such sites in the 28s and 18s ribosomal rrnas. 67 of these are known to undergo […]

PMCID: 4914119
PMID: 27174936
DOI: 10.1093/nar/gkw386

[…] study () for pseudouridine sites and from the newly developed rimseq method for 2′-o-methylation sites., at first, we predicted putative targets on human rrnas and snrnas using rnasnoop () and plexy () for human h/aca box and human c/d box snornas, respectively. precomputed rnaup structure profiles of target rnas () were provided to refine interaction predictions with rnasnoop. […]

PMCID: 4889943
PMID: 27016738
DOI: 10.1093/nar/gkw195

[…] in the text, in our population of 404 novel ncrna mcars, we instead identified 21 cd snornas. we examined for putative target sequences in these potential snornas at the known locations using plexy (). we attempted to identify putative h/aca snorna in a similar way but did not find criteria that enabled the identification of significantly more putative h/aca snorna in our novel ncrna […]

PMCID: 4748110
PMID: 26853913
DOI: 10.1038/ncomms10624

[…] confocal microscopy can better reveal the dynamic range of lexy., to test the robustness of lexy-mediated export when fused to different target proteins, we cloned two golden gate entry vectors plexy and pnls-lexy, both comprising a cytomegalovirus (cmv)-driven mcherry-lexy expression cassette carrying a bacterial toxin (ccdb) encoding gene at its 5′-terminus, flanked by bpii (bbsi) sites […]


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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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