PETcofold specifications

Information


Unique identifier OMICS_18683
Name PETcofold
Software type Package/Module
Interface Web user interface
Restrictions to use None
Input data Two RNA sequence alignments.
Input format FORMAT
Output data The input, phylogenetic tree, the PETcofold plain text output including the predicted joint RNA secondary structure and score, an image of the covariance and paired reliabilities in the concatenated RNA multiple alignment, and a dotplot of base pair and single stranded reliabilities calculated by PETcofold.
Computer skills Basic
Version 3.2
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Rolf Backofen <>
  • person_outline Jan Gorodkin <>
  • person_outline Stefan Seemann <>

Information


Unique identifier OMICS_18683
Name PETcofold
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Two RNA sequence alignments.
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Version 3.2
Stability Stable
Requirements
Pfold, the Vienna RNA Package
Maintained Yes

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Documentation


Maintainers


  • person_outline Rolf Backofen <>
  • person_outline Jan Gorodkin <>
  • person_outline Stefan Seemann <>

Publications for PETcofold

PETcofold in publications

 (6)
PMCID: 5408919
PMID: 27993777
DOI: 10.1093/bioinformatics/btw728

[…] defined as pseudo-energy minimization (). bistarna also includes accessibility and can predict multiple binding sites (). lastly, tools like targetrna2 (), coprarna (), miranda (), targetscan (), petcofold () and diana-microt () exploit homology and evolutionary conservation to predict interactions, some rna–rna interaction prediction tools are developed to achieve a specific task […]

PMCID: 5192221
PMID: 28004750
DOI: 10.1038/ncomms13875

[…] interaction site was computationally predicted to span the first exon of snhg5 and the 3′ utr of spats2. both the thermodynamics prediction (energy=−15.50 kcal mol−1; intarna) and the conservation (petcofold) point towards these regions as the interaction site. the interaction is only conserved among primates (phylogenetic tree predicted in petcofold) and the phylop base-wise conservation (100 […]

PMCID: 4838349
PMID: 26673718
DOI: 10.1093/nar/gkv1477

[…] type. the interaction-only and accessibility-based version of rnaplex can optionally take multiple sequence alignments as input, which we will denote as rnaplex-ca and rnaplex-aa, respectively. petcofold () belongs to the final complex joint structure category, given two multiple sequence alignment., mentioned above, the programs used are summarized in table , with more algorithmic details […]

PMCID: 4122056
PMID: 25114714
DOI: 10.1186/1748-7188-9-17

[…] integer programming. accordingly, it uses the approximate information of the internal and external base pairing probabilities of joint structures as an objective function of integer programming. petcofold [] employs covariance information in the internal and external base pairs to predict ssir of two multiple alignments of rna sequences. interna [] reduces the time and space complexity […]

PMCID: 4152356
PMID: 24755880
DOI: 10.4161/rna.28647

[…] by high-sequence conservation across related species,, comparative target prediction for conserved srnas appears to be a promising strategy to reduce the number of false positive predictions., petcofold was the first comparative method for the prediction of rna–rna interactions and joint secondary structures.- using two multiple alignments of rna sequences as input, petcofold predicts […]


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PETcofold institution(s)
Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, Faculty for Health and Medical Sciences, University of Copenhagen, Denmark; IBHV, University of Copenhagen, Denmark; Bioinformatics Group, University of Freiburg, Freiburg, Germany; Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna and University of Veterinary Medicine, Vienna, Austria; Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg, Germany
PETcofold funding source(s)
Supported by Lundbeck Foundation (grant 374/06); Danish Research Council for Technology and Production Sciences (grant 274-09-0282); Danish Center for Scientific Computation; German Federal Ministry of Education and Research (BMBF grant 0313921); German Research Foundation (DFG grants BA 2168/2-2 and BA 2168/4-1); Excellence Initiative of the German Federal and State Governments (grant EXC 294); Austrian GEN-AU project Bioinformatics Integration Network III and Wiener Wissenschafts-, Forschungsand Technologiefonds (WWTF) to the CIBIV Institute.

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